Well, the first way it would work is that sects are not necessarily part of the church.
The second way it works is that it was all written with the MMO in mind and then we won't have alignments anymore and only the mantras:Idealistic, Scholarly, Serious, Technological which doesn't necessarily imply good behavior as defined by the D&D Good/evil axis.
I didn't mention churches because churches have nothing to do with it. The "main church" of any god could just be the biggest and most popular sect, after all.
Yeah, that's probably better as a whole new thread (What Are Mantras Anyway?), along with another for my comments on how confusing it is to get MMO info without MMO rules.
I'm excited, too, but Acacea's old idea of decoupling NWN and MMO is still a good one.