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Well--Burning Heretics at the Stake, Witch Trials, Inquisition (Gallileo, Jordano Bruno, etc.), I suppose not Myths.

Church was (and still is to a certain extent) a primary patron of Arts, Sciences and Humanities--that's true. But we can't deny that it was at one time an oppressive force. Spanish Inquisition and Torquemada (Autonomous from Vatican but still Catholics) are not myths either. After all, why John Paul II chose apology to scientific and Jewish community for historical persecution, even though he had nothing to do with it ?

Actually I would rather not go too much into debate over this. It's hard to look into something (i.e. Christian Church History) objectively if you feel really passionate about it. What I'd rather do is to look forward when Christian Churches will truly become a potent moral force for good.

Well, since you mention it, really briefly:

The state viewed heresy as treason. The church was in charge of determining heretical views. It did not burn anyone, -- it would discuss the matter with the heretic and if he did not recant and failed to prove conformity, would "relax" him to the civil authorities who typically would execute him. There was nothing the church could do different.

When the state did not criminalize heresy, the church was content anathemizing it and not punishing the heretic corporately at all.

Gallileo and such were free to do science. When they ventured into domain of religion, their views were condemned inasmuch as their religious component was heretical. It is not unlike biologists today are condoned in their study of evolution, but condemned when their study is used to attack religion.

The church did things that were unwise. They should not have burned Savonarola, for example. It also did things that are horrific to us but were regular jurisprudence of the day. Often, better jurisprudence than what the secular authority had to offer. Cases are on record, -- with the famed Spanish Inquisition, -- when common thieves would pretend to be heretics so that they would fall under De Torquemada's jurisdiction rather than endure the secular trial.

In view of the scandals of the pederasty among priests today, I would very much advocate a return to the past practices of the Holy Inquisition in the United States. We have seen what happens when heretical, bordering on satanic views are tolerated among the priesthood. To tsk-tsk over the "persecution of the free thinkers" in the past is no ignore a log in our own eye.