I would like to emphasise that we often dramatically exaggerate the scale or the impact of given events and attitudes, whilst also diminishing their possible positives. We also tend to overexaggerate our infallibility.
Specific periods and events often had multiple factors, spanning from the obvious religion to as far as international politics.
You must imagine that for thousands of years religion has been a fairly dominant, well argued for, almost seemingly natural conclusion about reality. That there are many philosophers, scientists, and mathematicians etc., almost all of them had been religious. And they had been well argued in it. It is only today that we often believe that the arguments were poor, generally unreasoned, or otherwise. But some of the most prominent figures in the history of developing logic and the sciences... were extremely religious. Even some of the arguments they have now are fairly rigorous and thought out, you may believe them wrong - or be able to prove it so, but sometimes the person who comes along to come up with the argument for that, and popularise it, is several hundred years of thought away. It was not necessarily that religious people were only interested in systems of power and indoctrination, especially given that a lot of the most prominent figures, and origins of them, start with intentionally teaching the poor and housing them, etc., A lot of the monastic orders were established by peasants, and the intelligent among them were attracted to cosmic reasoning and argument.
One must imagine that you are suggesting you had it right compared to hundreds - thousands of years of pretty established figures detailing exactly why you did not. Furthermore, you have to imagine that you do not just have a different conception of God, but a complete disbelief or disregard for them. That said, this stance simply was not as uncommon as one may believe.
Atheism or indifference to the matter was fairly typical if one has more scrutinous standards. As far as I know, a good number of people, especially depending on time and place, did not pray, did not read the bible, did not adhere to many of the teachings (in any serious attempt), and were not particularly worried about divine retribution. It was more so that a very prominent and much larger amount of people were very serious about it. Very few people these days are very serious about anything.
Imagine being used as a political tool against your will, and being convinced of, and consequentially being dragged into the game of politicking. It is not as if these people had no innocence or rhyme or reason to them.
It is not too hard to imagine that when your entire life has been devoted and your belief is truly sincere, that crossing the Will of God would put some fury into a man's heart. You would do well to also remember that humans like to have an answer, even if they do not really believe it, or there is no apparent answer. A lot of people these days are identical. They follow majority consensus loosely, and are indifferent to it all. Complicit in the tragedies of the world.
It would be very hard to come up with an understanding and way to compartmentalise quite a few disorders. Imagine what it must feel like to see people of your village have spasms where they foam from the mouth, people that see things all the time, whisper to themselves, people who are hysterical and otherwise. Especially if it was your own child. Most people do not process trauma. They cope with it. One of the best ways to cope with it is to dehumanise, and functionally ignore / repress it.
It is no longer my Daughter, it is a daemon. The only thing that can help her is God. Religions tend to glamorise self-flagellation too. They compel you to a lot of self-sadistic attitudes. There is just a lot to consider, and I can definitely see how people would have made massive reaches to try and justify why their suffering exists, a test of faith, an abomination of the mind, something to purge. Something that explains why people suffer as they do, why they are so mentally affected.
And then you have to consider that yes, malicious people do exist. People who are self-interested. People who are simply accruing wealth and influence. It can be hard to resist the orders of massive structures of power, and it can be hard not to be complicit. Especially with pressure from all the wrong places. Even something as simple as misinformation can lead a very good person to some very dark places. You could be convinced to condemn your own daughter if people who are 'trustworthy' and 'educated' suggested, on their good word, she was responsible for grievous crimes.
Especially if you consider the kind of issues you could face if you defied things. This whole thing is not particularly coherent, but, hopefully it is understood.
You must also consider that persecution often leads to resistance. It often leads to the formulation of ideas, a new faith. I would not be so sure that we would have invented so and so much earlier. Usually, the idea foregoes the logic of the time, or the context of it. Innovation usually only comes from necessity. But more importantly, the Romans could have invented Steam Engines, but given the practicality of the time and effort of it, and the limited demonstrated scale of it, why would they assume that such would lead them to train engines faster and quicker. One must realise that even the rational mind can conclude in err with even just a lack of information, let alone misinformation.
