The persecutions are well documented. Most importantly I question the relationship these groups had to the modern day evangelic churches.
And I didn't read anything in the Wikipedia articles that said they were killed because the advocated they separation of church and state. You might say that is implicit but some of the protestant groups who left England to found the colonies did it for religious freedom for their sect alone. Certainly they differed from the state religion and were persecuted and killed for that but the Cathars for example held gnostic beliefs that would be unacceptable to almost all modern mainstream churches, though of course nobody is killed for that now.
I think you went too far in your claim. Had you said the Catholic church violently stamped out attempts to found christian churches that didn't accept their authority, no problem, I knew that.
lfen