Sounds like an awesome chronicle. In fact, it was the main story behind Neverwinter Nights 2 Mask of the Betrayer campaign. As for Mystara and Ilmater... they don't really have a choice but to be on board with it. Its what Ao decreed, and Ao isn't Good. Ao is True Neutral and a supporter of tyranny as well as freedom. So, you have the freedom to choose your tyrant. And, yes, in NW2 MotB we had an actual angel who felt the same way to the point she got kicked out of Mount Celestia.
Yeah, it can be annoying, but the gods hold as much sway over your story and plot that it only comes up if you make it. Take a look at the Brimstone Angels series. The dragonborn of Faerun don't worship gods, they think they're a bunch of tyrants, even the supposedly good ones. An entire society of aethists who are okay with ceasing to exist after they die.
Too bad that in MotB [Sblock]you don't get to shatter the Wall into pieces.[/Sblock] I enjoyed the game, but that was really disappointing.