Mass killings based on heretical beliefs or harmfully “seditious/treasonous” (including peaceful) ones were not solely a Catholic phenomenon, and neither side can claim a triumphant moral superiority. It’s a “wash.” 

Protestants engaged in religious persecution just as fiercely, if not more so, than Catholics had (and very often against each other). But they just happened to come along later in history and were around only 130-150 years before the time when both sides rapidly started deciding that all of this should stop. So we don’t have the many hundreds of years of “scandalous” Protestant “horror stories.”

It was a general characteristic of the age, which is why virtually everyone participated in it. In time — after about 130 years of Catholic vs. Protestant religious wars (1521-1651 or so) — people figured out that religious persecution was inadvisable and a non-starter. Virtually no one believes in it anymore. What I find objectionable is when Protestants try to imagine a fictitious, idealized, “scrubbed clean” past and argue that the early Protestants were — by nature — more tolerant of other viewpoints than Catholics were, and that they were basically proponents of religious freedom over against Catholics.

The nearly universal belief in the Middle Ages and up to at least the mid-17th century — and it does make sense — was that heresy was more dangerous than even murder, because it could cause people to be damned and go to hell; therefore, heretics ought to be persecuted at least as much as murderers. It was a sincere concern for the well-being of society and for souls (a thing few seem to even consider when condemning it). It usually had a good motivation, at least in theory, and a spiritual rationale beyond mere bloodthirstiness and grabs for power. And there is a surprisingly strong case that can be made for it from the Bible, that we must understand if we are ever to comprehend why these seemingly scandalous and sinful things happened in Church history. 

When we consult the Bible, we see that it taught capital punishment for all sorts of offenses, as part of Mosaic law, given by God to Moses (“his commandments and his statutes which are written in this book of the law” — Deuteronomy 30:10 [RSV]; “This book of the law shall not depart out of your mouth … be careful to do according to all that is written in it” — Joshua 1:8). The law was given by God to Moses on Mount Sinai. It was obviously his will. And part of that will were commands to execute those who rejected his commandments, including for false beliefs and immoral practices (i.e., “heresies”).

In other words, it’s not possible, biblically, to say that capital punishment is intrinsically or inherently wrong, because if it were, God could have never commanded it, since he can never sin or command immoral actions. Whether it is always best or good to permit it, and on the large scale that has been done, with excesses and corruptions, etc., is another huge discussion (I never favor any of this, just for the record), but we can’t declare it intrinsically wrong, because God didn’t do so.

In the Mosaic Law, there were more than 30 capital crimes. Several dealt with “heretical/false beliefs” — for example, sacrificing children to Moloch (Leviticus 20:1-2), worshiping Baal (Numbers 25:1-9), consulting mediums and wizards (Leviticus 20:6, 27), and following/worshiping “gods” other than Yahweh (idolatry and/or polytheism; Deuteronomy 17:2-7). There was even a penalty of burning, such as if a man had intercourse with both his wife and his wife’s mother (Leviticus 20:14), or if the daughter of a priest played the harlot (Leviticus 21:9). Both Catholics and Protestants also appealed to the many passages concerning God’s judgment and his commands to annihilate a certain portion of the population who were perceived to have — like Sodom and Gomorrah — sinned beyond redemption. Here is one:

If you hear in one of your cities, which the LORD your God gives you to dwell there, that certain base fellows have gone out among you and have drawn away the inhabitants of the city, saying, `Let us go and serve other gods,’ which you have not known, then you shall inquire ... if it be true and certain that such an abominable thing has been done among you, you shall surely put the inhabitants of that city to the sword, destroying it utterly, all who are in it and its cattle, with the edge of the sword. (Deuteronomy 13:12-15)

Note that God provided the explanation within the command: people had been “drawn away” by the prohibited and wicked polytheism and idolatry of certain people. To root out that sin, they had to be killed (at least at that early stage). Earlier in the chapter, God says that if a proclaimed prophet (even if his prediction comes true) says, “Let us go after other gods and let us serve them” (Deuteronomy 13:1-2), he “shall be put to death, because he has taught rebellion against the LORD your God … to make you leave the way in which the LORD your God commanded you to walk. So you shall purge the evil from the midst of you” (Deuteronomy 13:5).

God then commanded that the same death penalty be applied even to “brother … son … daughter, or the wife of your bosom, or your friend” (Deuteronomy 13:6-9). The reason is again provided: “because he sought to draw you away from the LORD your God” (Deuteronomy 13:10). This was the rationale — among both Catholics and Protestants — for all coercion and death penalties concerning false religious practices and beliefs. I don’t defend or condone religious persecution or coercion. But I try to understand it in its historical context, and to explain it, as a Christian apologist.