the fact that the empire just accept the altmer's fascist rule is not an argument in their favor

They had two choices, accept a ceasefire with some concessions so that they can build strength for the next war (this is literally just a waiting game the Imperials will win--humans breed faster than elves) or die. The Stormcloaks are being ridiculous babies and the thing they're maddest about, the enforcement of the ban on Talos worship, is something they themselves brought about. It wasn't being enforced until they started protesting about it and brought undue attention to the matter. They're just fucking idiot fascists, they don't understand the situation they're in at all and everything they do makes everything worse.

but the opposite - the altmer literally want to unmake reality.

This is a fringe conspiracy theory even among lore nerds. No one in-universe believes this to be the case and even from our bird's eye view of the situation there is very little evidence of this. But even assuming you're right, the Stormcloaks are making their success in this endeavor significantly more likely.

Also I'd like to point out that saying "the altmer" want to do this is really cringe and racist. Altmer are a race, made up of individuals. They aren't a hivemind and don't have a shared set of beliefs lol It would be like saying "The asians" want to do xyz when you're talking about Vietnam or India or something.