I generally find that heretic micromanagement is more of a pain than inquisitors. I had a piety 10 inquis. run around Spain for 40 years and he never touched my piety 3 heir in Zaragossa... Seems pretty random.

I recall that in the recent movie The Fountain, this bloodthirsty inquisitor is tried to kill Queen Isabella of Spain. Not that that means anything, but if it makes you feel better...