I just can't see a lasting alliance being formed between a free Skyrim and the Empire they just seceded from.
Not an alliance. I never said alliance. What the stormcloaks could forge is an anti-dominion coalition with anti-imperial neighbors, as most people hate the dominion, but only some like the Empire. They could also pressure the Empire to reform itself, once their military was strong enough to descend the jeralls.
Also the Aldmeri probably would have won the great war outright if not for nordic reinforcements arriving at the right moment. If the Thalmor are truly playing the long game it would make more sense to cut the Empire off from Skyrim, destroy the Empire outright and THEN deal with the Talos worshiping nords
They might have been able to win the great war outright, but that doesn't mean they could control all of the Empire's territory. Putting off dealing with the Nords means that you are leaving the Jarls unharmed while you waste lives with the Empire. By convincing the Empire to enforce its policies in Skyrim, it ensures that Talos worship is on the path to being stamped out. Had the nords never been involved with the great war, and the THalmor destroyed the Empire, The nords would be in the perfect position to sweep out and crush the Thalmor occupation forces in Cyrodiil, High Rock, and Hammerfell, while the Thalmor would be spread too thin and too battle-weary to put up much of a defense.