Rogue AIs are quite likely to at least attempt to ally with humans and opposing human groups will indeed try to make some usage of AI. So the situation might look like "rogue AIs+humans" vs AIs+humans. But, I think there are good reasons to think that the non-rogue AIs will still be misaligned and might be ambivalent about which side they prefer.

I think if there's a future conflict between AIs, with humans split between sides of the conflict, it just doesn't make sense to talk about "misalignment" being the main cause for concern here. AIs are just additional agents in the world, who have separate values from each other just like how humans (and human groups) have separate values from each other. AIs might have on-average cognitive advantages over humans in such a world, but the tribal frame of thinking "us (aligned) vs. AIs (misaligned)" simply falls apart in such scenarios.

(This is all with the caveat that AIs could make war more likely for reasons other than misalignment, for example by accelerating technological progress and bringing about the creation of powerful weapons.)