You wrote:
“Were these bad acts committed by the Protestant churches or were they committed by governments after passing laws outlawing the Roman Catholic Church?”
There was almost no difference between the two since the Protestant sects were created by, owned by, run by, and funded by the state.
“Youre not counting the actions of unruly mobs or over enthusiastic individuals acting on their own, are you?”
Nope.
“My ancestor witches were convicted by a secular court.”
That might be.
I'll remember that when I see the claims made by the Roman catholic Church that most of the deaths of the Inquisition took place after convictions in secular courts (under control of Catholic Monarchs).