Hey, one more idea, what about zoning religions?
When you have a temple of sufficient size you can declare it the headquarters of a diocese. Region lords with temples can decide which diocese their region belongs to in a manner similar to choosing duchies. The diocese with the largest temple is considered the arch diocese of the religion. The head of a diocese must be an elder and they have to be appointed at either the diocese headquarters or that of the whole religeon. The head of a diocese has the power to declare the temples under him independent of the arch diocese and thus a new religion.
Sooo pretty much a sect, that requires a temple of a certain size to set up the sect.