“At that time the Catholic church was as violent against the Protestants. Both sides were busy fighting religious wars.”
Yeah, but once side was fighting for what always was and the other was fighting to overthrow that.
The Catholic Queen Mary killed more Protestants in 5 years than Elizabeth did in her entire reign - and Elizabeth had greater cause, given the Catholic Church was trying to overthrow her.
As for “what always was” - the medieval Catholic Church fought to enlarge and enrich itself. It had a terrible record for anything slightly resembling honesty and integrity.