Hate to be the one to bring this up, but it seems there are two conflicting parties. This means that probably one of them will have to bite the dust.
Personally, I'dd stet something up that splits the story. Too keep it fun, for both groups, I'dd let the good PC's, valiantly, fight a losing battle, with the evil PC's in the background. But at the same time the good PC's should be able to find an escape mechanism that ltes them save their essence (you can define this however you want: culture, religion, gods, magic, ...) (i.e.: evacuating them to another plane outside of the influence of the evil PC's or by cutting of their part of the pmp, ...) That way, the good group can save whatever they find worth saving and the evil group can conquer and defile whatever they deem necessary. Or perhaps your goud group could find something that cuts of their world from the evil PC's. How their gods mix into this, I don't know...
If both groups would have been different players, a showdown between both parties would have been a great thing to work up to.