I think chaos did die... he became a spirit or something. His body was gone.
So basically the canon ending is out of question, then. Unless he can choose to stay behind, but apparently it isn't possible, since he used up his power of anime in that ending and that (imho?) caused "death".
(LOl I wrote "power of anime" xD It's so funny I decided not to fix it...)
So Shion should strike a deal with Wilhelm. Creative license sounds fine ^_^
Dammit, I don't see what to do, yet. I suppose she could strike a deal beforehand and then deceive him by refusing to comply, however, that would create the worst ending possible. And it doesn't make sense, I don't see Shion, let alone chaos, being fine with leaving things as they were. With half the planets been gone and Gnosis attacking and all that. One feels too much guilt for that, another is too kind.