The Catholic Church and Reformation churches felt obliged to kill heretics. The Reformers were more tolerant of heresy, as the earlier Reformers had been branded heretics themselves. But neither side allowed much in the way of dissent.
Both sides fought wars against the other, and both sides burned heretics. The battle between the two was particularly severe in France. This is from the Encyclopedia Britannica —
The Conspiracy of Amboise, formed by Huguenots [French Calvinists] with the object of kidnapping the boy-king Francis II (March 1560), resulted in the death of all the plotters except Louis I de Bourbon, Prince de Condé. But the Reformers had become so powerful that Gaspard de Coligny, their most famous leader, protested in their name at the assembly of notables at Fontainebleau (August 1560) against all violation of the liberty of conscience. The attempt at peace failed. After a number of Huguenots assembling for worship in a barn at Vassy were massacred by soldiers of the Roman Catholic Guise family, Condé declared that there was no hope but in God and arms. At Orléans on April 12, 1562, the Huguenot leaders signed the manifesto in which they stated that as loyal subjects they were driven to take up arms for liberty of conscience on behalf of the persecuted saints.
Thus began a period of confusion and violence in France, known as the Wars of Religion, that lasted until almost the end of the century. A famous incident of this period was the Massacre of St. Bartholomew’s Day. On the night of Aug. 24/25, 1572, after a council at which the queen mother Catherine de Médicis, King Charles IX, the Duke d’Anjou (later Henry III), and the Guises were present, there occurred a massacre in which Coligny and almost all the leading Huguenots in Paris were slain. The Paris massacre was repeated throughout France, and Protestants were slain in thousands. The Protestant survivors resolved upon a desperate resistance, and a Huguenot political party was formed at Milhaud, near Nîmes, in 1573. Especially prominent was Philippe de Mornay, known as Duplessis-Mornay. The Huguenots at first hoped that the crown of France would pass to a Huguenot; when that became obviously impossible, they fought for full religious and civil liberty within the state.
War was resumed after the Massacre of St. Bartholomew’s Day and continued, with short-lived intermissions, throughout the reign of the unpopular Henry III, who succeeded Charles IX in 1574. Henry’s hesitations encouraged the formation of the powerful Holy League against the Huguenots; and, after the assassination of Henry III in 1589, his successor, the Protestant heir Henry IV, could pacify the kingdom only by adjuring Protestantism (July 1593), accepting Catholicism, and thus depriving the League of its pretext for resisting him. The Huguenots after 40 years of strife obtained by their constancy Henry IV’s promulgation of the Edict of Nantes (April 1598), the charter of their religious and political freedom.
Civil wars, however, occurred again in the 1620s under King Louis XIII. Eventually the Huguenots were defeated, and the Peace of Alès was signed on June 28, 1629, whereby the Huguenots were allowed to retain their freedom of conscience but lost all their military advantages. No longer a political entity, the Huguenots became loyal subjects of the king. Their remaining rights under the Edict of Nantes were confirmed by a royal declaration in 1643 on behalf of the infant king, Louis XIV.
The French Roman Catholic clergy, however, could not accept the Huguenots and worked to deprive them of their rights. General harassment and the forcible conversion of thousands of Protestants were rampant for many years. Finally, on Oct. 18, 1685, Louis XIV pronounced the revocation of the Edict of Nantes. As a result, over the next several years, France lost more than 400,000 of its Protestant inhabitants. Many emigrated to England, Prussia, the Netherlands, and America and became very useful citizens of their adopted countries. Many were urban people in commerce and industry, and their absence would hurt France in the coming Industrial Revolution.
The article sanitizes the story. As each faction gained political control of a town, they declared the other side to be heretics, prevented their assemblies, and often resorted to torture to make the point. The Wikipedia says,
Amidst fears of a Huguenot coup, the Duke of Guise and his supporters acted and, in the early morning of August 24, killed Coligny in his lodgings with several of his men. Coligny’s body was thrown from the window into the street, and was subsequently mutilated, castrated, dragged through the mud, thrown in the river, suspended on a gallows and burned by the Parisian crowd. For the next five days the city erupted into a full-scale massacre of Calvinist men, women and children, and the looting of their houses, which was neither approved of nor predicted by the king. Over the next few weeks the disorder spread to more than a dozen cities across France. Perhaps 2,000 Huguenots were slaughtered in Paris and, in the days that followed, thousands more in the provinces; in all, perhaps 10,000 people were killed. Henry of Navarre and his cousin, the young prince of Condé, managed to avoid death by agreeing to convert to Catholicism; both would repudiate their conversions once they managed to escape Paris.
Both Philip II of Spain and Pope Gregory XIII declared themselves pleased with the outcome, which provoked horror and outrage by their religious opponents throughout Europe. In France, Huguenot opposition to the crown was left seriously weakened.
The ‘fourth’ war (1572–73)
The massacres set off further military action, which included Catholic sieges of the cities of Sommières (by troops led by Henri I de Montmorency), Sancerre and La Rochelle (by troops led by the duke of Anjou). The end of hostilities was brought on by the election (11 – 15 May 1573) of the Duke of Anjou to the throne of Poland and by the Edict of Boulogne (signed in July 1573) which severely curtailed many of the rights previously granted to French Protestants. Based on the terms of the treaty, all Huguenots were granted amnesty for their past actions and the freedom of belief. However, they were permitted the freedom to worship only within the three towns of La Rochelle, Montauban, and Nîmes, and even then only within their own residences; Protestant aristocrats with the right of high-justice were permitted to celebrate marriages and baptisms, but only before an assembly limited to ten persons outside of their family. 
Again, these quotes understate the brutality with which the two sides treated each other. In fact, eventually France banned Protestantism entirely, driving the Huguenots out of the country, with many fleeing to the U.S. and other parts of Europe.
The abominable behavior of both sides reverberated across the English channel, leading to the Enlightenment and the idea of freedom of religion. The theory developed by British philosophers was to separate church from state and to allow citizens the right of individual conscience — so the Christians would stop killing each other. In fact, the horrors visited on the sides by the other were so great that modern day atheism finds its roots in the religious wars of France.
The United States was founded by people fleeing religious persecution in Europe. We never really studied the European persecution in school — just the results in America. And so, following the Enlightenment solution, many states adopted constitutions guarantying freedom of religion. Nonetheless, the old animosities didn’t die. Rather, while the Christians did stop killing each other, they did continue to damn over any imperfect in doctrine at all.
Meanwhile, in Scotland, John Knox, a disciple of Calvin, founded the Presbyterian Church. By 1560 the First Book of Discipline was written and the Church of Scotland was born.
Division took place, between Seceder and Non-Seceder churches in 1712. Seceder Presbyterians selected their own ministers. Anti-Seceder Presbyterians had their ministers selected by high-church counsel.
Another split arose in the Burgher movement in 1747 over whether the burgesses (mayors) of the Scottish cities could swear to support the established churches. Thus, a mayor could decide for the city if the city would be a Seceder Church or Anti-Seceder Church.
The Burgher movement then split over people should be amenable to “new light” from Scripture or should be strictly limited to the Westminster Confession of Faith.
In short, by time of Thomas Campbell, there were 8 kinds of Presbyterians, and each sect damned the other. Campbell was a minister of the Old-Light Anti-Burgher Seceder Presbyterian Church. He was a Presbyterian that thought they should select their own minister, and the mayor of the city should have nothing to do with it, holding to the original interpretation of the Westminister Confession of Faith concerning the power of civil magistrates in religion.
When Campbell immigrated to Pennsylvania as a Prebyterian minister, he found that many Presbyterians in western Pennsylvania hadn’t received communion for years because there was no church of their particular persuasion in the area. Campbell figured that the political fights of Scotland had nothing to do with pastoring God’s people, and so he served them communion. And so he was tried and excommunicated.
This lead to his writing the “Declaration and Address,” in which he concluded,
5. That with respect to the commands and ordinances of our Lord Jesus Christ, where the scriptures are silent, as to the express time or manner of performance, if any such there be; no human authority has power to interfere, in order to supply the supposed deficiency, by making laws for the church; nor can any thing more be required of christians in such cases, but only that they so observe these commands and ordinances, as will evidently answer the de- clared and obvious end of their institution. Much less has any human authority power to impose new commands or ordinances upon the church, which our Lord Jesus Christ has not enjoined. Nothing ought to be received into the faith or worship of the church; or be made a term of communion amongst christians, that is not as old as the New Testament.
6. That although inferences and deductions from scripture premises, when fairly inferred, may be truly called the doctrine of God’s holy word: yet are they not formally binding upon the consciences of christians farther than they perceive the connection, and evident ly see that they are so; for their faith must not stand in the wisdom of men; but in the power and veracity of God–therefore no such deductions can be made terms of communion, but do properly belong to the after and progressive edification of the church. Hence it is evident that no such deductions or inferential truths ought to have any place in the churchs’s confession.
7. That although doctrinal exhibitions of the great system of divine truths, and defensive testimonies in opposition to prevailing errors, be highly expedient; and the more full and explicit they be, for those purposes, the better; yet, as these must be in a great measure the effect of human reasoning, and of course must contain many inferential truths, they ought not to be made terms of christian communion: unless we suppose, what is contrary to fact, that none have a right to the communion of the church, but such as possess a very clear and decisive judgment; or are come to a very high degree of doctrinal information; whereas the church from the beginning did, and ever will, consist of little children and young men, as well as fathers.
Nowadays, it’s common to feel as Campbell did. 21st Century Americans are very non-denominational in their thinking. And so we don’t really see how revolutionary Campbell’s ideas were. But this idea was unheard of in its day. No one had thought like this since, well, before Constantine. You see, the Restoration Movement was originally not about baptism or instrumental music. It was about unity based on a common faith in Jesus. Period.
Ultimately, he and his son, Alexander, concluded that faith in Jesus and a willingness to obey his commands is all that’s required to be saved and to be entitled to be recognized as a fellow Christian. It’s no wonder their movement grew rapidly, dramatically changing the face of America.