And the violence in France was not committed by the Catholic church any more than the violence againts Catholics in England was committed by the Anglican Church. All over Europe in the 1500s kings were consolidating absolute power. The Protestant-Catholic conflict from 1546-1648 was state conflict in which princes chose sides in a religious dispute and turned it into political war. If the princes had no chosen sides the religious dispute with Luther might well have been resolved.
No where is this more visible than in France where men ambitious for the crown thought nothing of switching from Protestant to Catholic and back if they thought it would benefit their power grab.
Every historian of Spain in this period agrees that the kings took over the church courts to use the Inquisition as an instrument of state power. Popes protested the abuse of power by the kings. The most advanced system of justice in Europe at the time was in the Roman Inquisition in the Papal States where you had better due process protection (knowledge of who your accuser was etc.) than under Henry VIII with his Star Chamber court or where he simply executed people without trial: after failing to intimidate the London Carthusian monks by, after show-trials, disemboweling two batches of their leaders and earning public opprobrium for butchering innocent and highly respected holy men, he gave up and simply shackled the last batch to dungeon walls without trial and left them to starve. Margaret Roper, Thomas More’s daughter, bribed the jailers to be able to feed them—Henry got suspicious because they were taking too long to die and put an end to her ministrations and they eventually died wretchedly.
Are you Protestant-proud of all that yet?
The affair of Luther would have also ended with his being burned, had not some German princes protected him. There was no resolution between Rome and Luther because the theological dispute was fundamental. Then, and even now, the RCC promoted beliefs which have no scriptural basis and are in fact contrary to scripture.
The historical facts do not allow contradiction, despite the complications you introduce to blur the issue. Free societies with limited government and freedom of religion did not arise in any Catholic country. They arose in England and a few other Reformed countries as logical consequences of Reformation thinking about the individual, his conscience, and his reliance on written scripture alone. Rome regarded the Bible as liberals regard the Constitution: as a living, breathing document they could add to or modify as the hierarchy chose.