The first Papal Bull that is known to have called for the punishment of specific heretics is Ad Abolendam (1184 AD), issued by Pope Lucius III (1097-1185 AD). It was incorporated into Canon 3 of the Fourth Lateran Council:
Fourth Lateran Council (1215 AD)
3 We excommunicate and anathematize every heresy raising itself up against this holy, orthodox and catholic faith which we have expounded above. We condemn all heretics, whatever names they may go under. They have different faces indeed but their tails are tied together inasmuch as they are alike in their pride. Let those condemned be handed over to the secular authorities present, or to their bailiffs, for due punishment.
Let secular authorities, whatever offices they may be discharging, be advised and urged and if necessary be compelled by ecclesiastical censure, if they wish to be reputed and held to be faithful, to take publicly an oath for the defence of the faith to the effect that they will seek, in so far as they can, to expel from the lands subject to their jurisdiction all heretics designated by the church in good faith. Thus whenever anyone is promoted to spiritual or temporal authority, he shall be obliged to confirm this article with an oath. If however a temporal lord, required and instructed by the church, neglects to cleanse his territory of this heretical filth, he shall be bound with the bond of excommunication by the metropolitan and other bishops of the province.
Catholics who take the cross and gird themselves up for the expulsion of heretics shall enjoy the same indulgence, and be strengthened by the same holy privilege, as is granted to those who go to the aid of the holy Land. Moreover, we determine to subject to excommunication believers who receive, defend or support heretics.
Notice that the Church worked closely with the state to ensure that heretics were punished. Also, notice that the same Indulgence promised to the Crusaders (mentioned later in the same council) will be given to those who reprimand heretics. This is significant, because in Roman Catholic theology, Indulgences are an exercise of the power of the Keys (Matthew 16:19). This means that this council is promising a God-sanctioned remission of guilt, founded upon the office of the Papacy, in exchange for persecuting heretics.
A few years after the Fourth Lateran Council, Pope Gregory IX (1170-1241 AD) would issue Ille Hamni Generis (1232 AD), which is generally regarded as having officially started what would come to be known as the Inquisition. It, along with Licet ad Capiendos (1233 AD), appointed the Dominicans and Franciscans to organize the Inquisition in France, Italy, and Germany.
This would be followed over the subsequent centuries by many other Papal Bulls, which created or re-established the Inquisition, or crusades against heretics, in various countries, a semi-complete list being:
Some of these Inquisitions would go on to last for hundreds of years. The Spanish Inquisition, by far the most infamous of them all, was enabled by the issuing of Exigit Sinceræ Devotionis (1478 AD) by Pope Sixtus IV (1414-1484 AD), and would last until 1834 AD - over 350 years.
One of the above, Ad Extirpanda (1252 AD), given by Pope Innocent IV (1195-1254 AD), again demonstrated how the Church worked with the state to criminalize those that it deemed to be heretics:
Pope Innocent IV - Ad Extirpanda (1252 AD)
2 At the commencement of his term of office... the head of state or ruler of the city or feudal domain shall accuse of criminal conduct all heretics of both sexes, no matter by what name they appear on the rolls of citizens. And he will confirm his right to the office inherited from his predecessor in this manner. And furthermore, that no heretical man or woman may dwell, sojourn, or maintain a bare subsistence in the country, or any kind of jurisdiction or district belonging to it, whoever shall find the heretical man or woman shall boldly seize, with impunity, all his or their goods, and freely carry them off, to belong to the remover with full right, unless this kind of removing is restricted to persons designated by law.
The blame for the Inquisitions cannot be offloaded onto the secular authorities, because the Church demanded that they criminalize heretics, and of course, the Church was the one giving the state their definition of "heresy" in the first place. Biblically, this implicates them directly, as if they themselves were doing the killing (2 Samuel 12:9).
This Papal Bull also mandated the torture of heretics, in order to compel them to confess:
Pope Innocent IV - Ad Extirpanda (1252 AD)
25 The head of state or ruler must force all the heretics whom he has in custody, provided he does so without killing them or breaking their arms or legs, as actual robbers and murderers of souls and thieves of the sacraments of God and Christian faith, to confess their errors and accuse other heretics whom they know, and specify their motives, and those whom they have seduced, and those who have lodged them and defended them, as thieves and robbers of material goods are made to accuse their accomplices and confess the crimes they have committed.
Notice how utterly different the above commandment is to the commandments that we receive in Scripture for dealing with those who disagree with us on doctrine (2 Timothy 2:24-26: 2 Thessalonians 3:14-15, Colossians 4:5-6). On this matter of faith and morals, the Bible tells us to "mark and avoid" heretics (Romans 16:17), not criminalize them, torture them, and then remand them to the authorities for punishment.
Those who gave refuge to heretics were also to receive severe punishment:
Pope Innocent IV - Ad Extirpanda (1252 AD)
26 And the house, in which a male or female heretic shall be discovered, shall be levelled with the ground, never to be rebuilt; unless it is the master of the house who shall have arranged the discovery of the heretics. And if the master of the house owns other houses in the same neighbourhood, all of the other houses shall in like manner be destroyed, and the goods that shall be found in the house and the others related to it shall be dispersed to the populace, and shall belong to whoever carries them off, unless the removers shall be appointed by law. Above all, the master of the house, besides incurring eternal infamy, must pay the government or locality fifty pounds Imperial in coin; if unable to pay, he shall suffer life imprisonment. The borough where the heretics are arrested or discovered shall pay the government of the state a hundred pounds; and a manor shall pay fifty, and the regions adjoining manors and states, fifty.
The entire text of this Papal Bull contains many statements like the above. Those who helped, or listened to heretics, would receive the same kinds of punishments as heretics, and they were to be severe.
One notable heretic who was killed in the midst of all of this was the Proto-Protestant Jan Hus, who was burned at the stake in 1415 AD after being condemned by the Council of Constance (1414-1418 AD). The burning of Jan Hus, and others like him, was defended during the time of Martin Luther, in Pope Leo X's (1475-1521 AD) list of errors:
Pope Leo X - Exsurge Domine (1520 AD)
33 That heretics be burned is against the will of the Spirit. (Condemned)
Taking all of the above into account, it's apparent that the Catholic Church actively and brutally persecuted those who disagreed with it on matters of doctrine, and that the fate of those deemed heretics by the Roman Catholic Church was often horrific.
The declarations of the Second Vatican Council (1962-65 AD) changed a lot in the Roman Catholic Church. It changed so much, so clearly, that some traditionalist Catholics formed Sedevacantist groups, which declare the Council heretical, and accuse all subsequent Popes of being Antipopes which have abandoned the Catholic faith.
This change extended to the matter in question, namely, how the Church is to deal with heretics, and the subject of religious liberty more broadly.
One of its declarations is entitled Dignitatus Humanae - Declaration on Religious Freedom. In it, we read:
Vatican 2 (1965 AD) - Dignitatus Humanae
2 This Vatican Council declares that the human person has a right to religious freedom. This freedom means that all men are to be immune from coercion on the part of individuals or of social groups and of any human power, in such wise that no one is to be forced to act in a manner contrary to his own beliefs, whether privately or publicly, whether alone or in association with others, within due limits.
The council further declares that the right to religious freedom has its foundation in the very dignity of the human person as this dignity is known through the revealed word of God and by reason itself. This right of the human person to religious freedom is to be recognized in the constitutional law whereby society is governed and thus it is to become a civil right.
The above, in light of Catholic history covered in the preceding section, is an inarguable contradiction, because it is declaring that "the right to religious freedom" has its basis in the dignity of mankind itself, and "is known through the revealed word of God and by reason itself". Likewise, "all men are to be immune from coercion" in religious matters.
Yet, the same Church has historically, and infallibly, taught that people must be "coerced" (tortured, besieged in crusades, persecuted) for holding beliefs that it deemed to be heretical. These are clear, irreconcilable, contradictions.
The entire declaration is consistent and explicit in establishing the principles of freedom of conscience in religious matters, and the right to religious freedom:
Vatican 2 (1965 AD) - Dignitatus Humanae
3 Wherefore every man has the duty, and therefore the right, to seek the truth in matters religious in order that he may with prudence form for himself right and true judgments of conscience, under use of all suitable means. On his part, man perceives and acknowledges the imperatives of the divine law through the mediation of conscience. In all his activity a man is bound to follow his conscience in order that he may come to God, the end and purpose of life. It follows that he is not to be forced to act in a manner contrary to his conscience. Nor, on the other hand, is he to be restrained from acting in accordance with his conscience, especially in matters religious.
Injury therefore is done to the human person and to the very order established by God for human life, if the free exercise of religion is denied in society, provided just public order is observed.
6 It follows that a wrong is done when government imposes upon its people, by force or fear or other means, the profession or repudiation of any religion, or when it hinders men from joining or leaving a religious community. All the more is it a violation of the will of God and of the sacred rights of the person and the family of nations when force is brought to bear in any way in order to destroy or repress religion, either in the whole of mankind or in a particular country or in a definite community.
10 It is one of the major tenets of Catholic doctrine that man's response to God in faith must be free: no one therefore is to be forced to embrace the Christian faith against his own will. This doctrine is contained in the word of God and it was constantly proclaimed by the Fathers of the Church.
And, the same sentiment of Dignitatus Humanae is echoed in another of Vatican 2's declarations, Nostra Aetate:
Vatican 2 (1965 AD) - Nostra Aetate
5 The Church reproves, as foreign to the mind of Christ, any discrimination against men or harassment of them because of their race, color, condition of life, or religion.
The above statements declare the actions of former Popes and councils to have done "injury... to the human person, and to the very order established by God for human life", to have acted in "violation of the will of God and of the sacred rights of the person", and to have acted in ways "foreign to the mind of Christ". As is obvious, this is in direct contradiction to historic Catholic doctrine, taught and implemented for many hundreds of years, and ordered by many "Vicars of Jesus Christ", along with ecumenical councils.
Also, in establishing the principle of freedom of conscience in religious matters, it further directly contradicts Pope Pius IX's (1792-1878 AD) famous Syllabus of Errors:
Pope Pius IX - Quanta Cura (1864 AD), Syllabus of Errors
77 In the present day it is no longer expedient that the Catholic religion should be held as the only religion of the State, to the exclusion of all other forms of worship. (Condemned)
78 Hence it has been wisely decided by law, in some Catholic countries, that persons coming to reside therein shall enjoy the public exercise of their own peculiar worship. (Condemned)
79 Moreover, it is false that the civil liberty of every form of worship, and the full power, given to all, of overtly and publicly manifesting any opinions whatsoever and thoughts, conduce more easily to corrupt the morals and minds of the people, and to propagate the pest of indifferentism. (Condemned)
In the main body of the Encyclical, he also says:
Pope Pius IX - Quanta Cura (1864 AD)
3 And, against the doctrine of Scripture, of the Church, and of the Holy Fathers, they do not hesitate to assert that “that is the best condition of civil society, in which no duty is recognized, as attached to the civil power, of restraining by enacted penalties, offenders against the Catholic religion, except so far as public peace may require.” From which totally false idea of social government they do not fear to foster that erroneous opinion, most fatal in its effects on the Catholic Church and the salvation of souls, called by Our Predecessor, Gregory XVI, an “insanity,” namely, that “liberty of conscience and worship is each man’s personal right, which ought to be legally proclaimed and asserted in every rightly constituted society; and that a right resides in the citizens to an absolute liberty, which should be restrained by no authority whether ecclesiastical or civil, whereby they may be able openly and publicly to manifest and declare any of their ideas whatever, either by word of mouth, by the press, or in any other way.” But, while they rashly affirm this, they do not think and consider that they are preaching “liberty of perdition;” and that “if human arguments are always allowed free room for discussion, there will never be wanting men who will dare to resist truth, and to trust in the flowing speech of human wisdom; whereas we know, from the very teaching of our Lord Jesus Christ, how carefully Christian faith and wisdom should avoid this most injurious babbling.”
6 Therefore, by our Apostolic authority, we reprobate, proscribe, and condemn all the singular and evil opinions and doctrines severally mentioned in this letter, and will and command that they be thoroughly held by all children of the Catholic Church as reprobated, proscribed and condemned.
Above, Pope Pius IX condemns exactly the kind of religious liberty that Vatican 2 established as a fundamental human right, given by God. And, as the final section above shows, this was an Ex Cathedra statement.
Pius IX also referenced Pope Gregory XVI (1765-1846 AD) above, who said:
Pope Gregory XVI - Mirari Vos (1832 AD)
14 This shameful font of indifferentism gives rise to that absurd and erroneous proposition which claims that liberty of conscience must be maintained for everyone. It spreads ruin in sacred and civil affairs, though some repeat over and over again with the greatest impudence that some advantage accrues to religion from it. “But the death of the soul is worse than freedom of error,” as Augustine was wont to say.
15 Here We must include that harmful and never sufficiently denounced freedom to publish any writings whatever and disseminate them to the people, which some dare to demand and promote with so great a clamor. We are horrified to see what monstrous doctrines and prodigious errors are disseminated far and wide in countless books, pamphlets, and other writings which, though small in weight, are very great in malice.
The amount of Catholic history which is so clearly and unambiguously overthrown and reprobated by Vatican 2 is striking. Papal Bulls, Encyclicals, local councils, ecumenical councils, and the actual practice of the Church's agents and leaders, are all condemned as contrary to God, the Bible, and the fundamental dignity of mankind.
Historically, the Catholic Church infallibly taught that the persecution, torture, and execution of those who disagreed with it on doctrinal matters, was Biblically proper. The same Church, in modern times, infallibly teaches that religious freedom is a God-given human right, and decries any attempt to suppress religious freedom. All the while, it maintains that it has never erred (Pope Gregory VII - Dictatus Papae 22, etc.).
These claims are meaningless, and indisputably false. The Catholic Church has simply contradicted itself, as is obvious to anyone having their eyes still open to the truth. Diving into Church history reveals case after case of such contradiction, and this one in particular resulted in such an incredible amount of suffering.