The thing about CoS on FEI is that there just aren't enough people in it that are devoted to it enough to try and buck the system. It suffers what most BM religions suffer: It is full of people that don't care about it. They are there for political reasons, or really no reason at all. If the leaders of the religion tried to do anything remotely controversial that would hurt the political position of their members, a significant portion of those members would just refuse to participate, or outright leave to find some other, blander religion.
I don't think that a CoS on BT would escape this problem, either. (We are seeing this begin on Dwilight now with SA as well.) Melhed tried to have a religion that would take a more prominent role in running the government, didn't they? And IIRC, that religion was one of the reasons Thalmarkin went after them.