Historically, many bishops were appointed by lords (free investiture was a particular quarrel between the Holy Roman Empire and the Papacy and appointment to a bishopric was a handy way to disinherit sons) so I don't see it as too odd that the lord would have appointed the priest at his local temple. Converting the temple but not the peasants allows priests of the parent religion to strike back by whipping the local population into a furor while striking a compromise between who the church "belongs to" and what the peasants believe.
You could have a roll similar to what happens when nobles raid temples that allows the locals to stop the priests they like from being replaced, if you wanted. That way a schism would require coordination between nobles in the schismatic sect to take control of the temples with extra troops or some such (I assume quantity of troops affects the outcome of that roll).
I don't mind it being automatic that all nobles join when schism is declared; if you go into it knowing that as a player then your character should also know that he is placing his soul in the hands of the leader of his sect. And this way if the noble wants to go back, his region already follows the old religion and tearing down and replacing (or rededicating if that gets implemented) the temple should take only time and gold.
Except that there's no such thing as striking back with a furor. Even in a region with 95% following, poor stats, and monsters, a priest with 100 oratory fame can't seem to achieve squat. And when you try too long, the local population gets tired of you as a bonus to achieving nothing.
