If you share a common enemy you should unite to overcome the enemy. In this case the empire did sell out to the AD, but only as a necessity to survive. They did sell out the Nord religion, alienating the Nords as a result, and they sold out the Redguards, I'm not going to dispute that. But you have to think the empire still resents the AD after everything they did to them during the war. If Skyrim becomes independent they are that much easier for the high elves to conquer. The banner of the empire gives them some protection and if the empire can get stronger they have that much more chance to one day resist the AD. Basically, becoming independent weakens them, it weakens the empire, and it probably would ultimately benefit the AD as a reult.
In times of war you some times have to swallow your pride for the greater good of future generations by uniting with an enemy to overcome a greater enemy. The elves are assholes, so gain strength by uniting and stomp out your common enemy.
Stormcloack is a short-sighted warmongerer.
But
I can see both sides. No culture should be persecuted for their religion and the empire really is showing no backbone. And you could argue the AD fear the Nords, which is why they want to put an end to the rebellion (though I think it's really just the AD flexing trying to force the 'superior race' thing by trying to stomp out mention of gods that are men; not necessarily because they fear an independent Skyrim). Just the pros cons of each side still point me towards the empire.
That's what makes the game so interesting, you can make a case for either side which makes replaying on the other side still fun.