Illusions are designed to interfere with alliance, as such, i think it's even a necessity that the old ally status gets reset when the illusion ends.
I've had wodin's guard in my ally, who is unkickable because it's an illusion, but he can't do anything inside, either.
It would be extremely annoying if you were illusioned for some days to play on a mission, as illusions are set, and then find yourself stripped from your real alliance while being unable to do something about it, which is obviously a very special problem for leaders.
If an ally member goes disguised for a while, they're still members, but can't do anything inside during the time disguised. It would be highly unfair if a person could be kicked from their real ally while they are stuck in the illusion ally, even more so if the person kicked is the leader of an ally.
When Peace kicked me from my ally, i wasn't happy about it, either, but that was fair and square, i could've gotten a higher loyalty count to stop her. If I do everything in my power, and still lose, fine. But if i lose without having a chance to fight, that's not fine.