The medieval church may have been a necessary evil in the progress of the West, but it was still evil. It’s worth reviewing how that happened, because it represents a pattern. Quite simply, when individuals are forced to conform to the institution, rather than the institution to the individual, the institution starts down the path toward evil.
The Roman Empire was formed atop of many nations and the Romans often just incorporated the local god into their pantheon of gods. Religious tolerance was a given and variation expected.
We now know that in the centuries after Christ, a great number of gospels and letters emerged. Some of these, like the Gospels of Thomas and Judas, had disappeared completely until discoveries just last century.
But this variation that was a part of the ancient world was squelched. Forcefully. The Inquisition was instituted in 1233 and by 1252 the church had authorized the use of torture to impose conformity of thought. As late as 1600, Giordano Bruno was burned alive for sharing his beliefs about moving atoms, an infinite cosmos, memory, and imagination. The goal was to crush heresy, defined as any dissent or deviation from Church teachings, and the Church was not squeamish about the use of force to protect its dogma. Over the centuries, the treatment of heretics included the rack (being stretched until every joint in the body had dislocated), burning at the stake, and being skinned alive.
Torture was consistent with the teachings of St. Augustine, who felt that the “main point was ‘not whether anyone is being forced to do something, but what sort of thing he is being forced to do, whether it is good or bad.’” Punishment was justified “because ‘the unrighteous man’s grief in his punishment is more appropriate than his rejoicing in sin.’” Torture was of little consequence in comparison to an eternity in hell: if pain caused one to recant from heresy, it was a gift. Once a community accepts the notion of one truth about eternal salvation and one authority entrusted with its revelation, every kind of coercion and evil naturally follow.
How did the church become evil? By suppressing variation and oppressing the individual. This is always the surest route to evil, no matter how petty the path. It is possible that it was a necessary evil but it bears repeating that it was, in any case, an evil. Any institution able to seize one's property or children and torture or kill to coerce thought and belief can hardly be given any other label.
The evil crept into the church in small steps. It wasn't evil for individuals to say, "I believe the gospel of Matthew but not the gospel of Thomas." It didn't seem particularly evil for a group of individuals to get together in a council to reach an agreement about which books to include and which to exclude to promote a "right" way. And once that was in place, it did not seem so evil to urge conformity on the congregation, or to resort to expulsion or even violence to spare the congregation from the influence of a heretic (simply someone whose beliefs are not orthodox). Over centuries, though, the cumulative effect of these little steps became clear.
And this meant that before real progress could begin in the West, the church had to be radically changed. The revolution that overturned its monopoly on thought and action would prove even bloodier than its oppression. Encompassed in the Protestant Revolution and Reformation, this challenge to the medieval church gave birth to a new world with new rules, one that offered the individual opportunities never before given to the common man.