I don't have a problem with heresy being criminalized, at least in theory. Heresy leads to death, both spiritually and physically, so it falls within the competence of the State, whose primary duty is the protection of the lives of its citizens. In practice, the usefulness of prosecution has passed, since it is literally impossible to slow the spread of heresy given our modern means of communication.
One important distinction between the acts of Catholic and Protestant rulers regarding the prosecution of heretics is that there was no distinction between State and Church in Protestant lands. Those suffering from abuse at the hands of the Protestant State could not appeal to the Protestant Church, since there was no distinction between the two.
Protestantism evolved into national churches from its inception, in direct conflict with the universal mission of Christ's Church (John 17:21).
Do you think Christ had enough power to eliminate all heresies from the country he lived in, so that only his correct teachings would be the ones spread?
Hurry, we must summon the Dominicans.