The right exists for authorities to punish criminals, whether in the ecclesiatical or secular realm. After the destuction of Christendom, the idea of temporal punishment for spiritual crimes became less common and is therefore viewed in modern times as barbaric, whereas the Inquisition saw it as an act of mercy to effect repentance when all other means had failed. The death of the soul through heresy (understanding the effects of mortal sin) is infinitely worse than the death of the body. "For what shall it profit a man, if he gain the whole world, and suffer the loss of his soul?"
"The right exists for authorities to punish criminals, whether in the ecclesiatical or secular realm."
But when the bar of what quantifies a "criminal" is lowered to such a point that only a saint could get under it, the notion becomes intolerable.
Authorities have no rights, only powers granted to them by the people. The people cannot, however, legitimately grant the authorities the power to violate inalienable rights. Any government that does that deserves nothing but violence and resistance directed at it and its representatives.