Okay that clears things up a bit. I didn't realise..
Still, this is showing part of the problem in the idea. An Assembly is a democratic process and a very human one at that. By having one, you are humanising the gods, turning them into something human. Implying a chain of command and all the rest that follows...
I just don't think it works like that. I could be wrong of course... but if we do this, there is no getting away from them being 'humans with powers'. Just by doing it.