The Empire (Skyrim, High Rock, Cyrodiil and others I currently can't recall) DID quell the Thalmor threat. Ish. They didn't fail, which I suppose is good. And the war was ended with a truce.
But can Cyrodiil and Skyrim together pose a larger threat to the Empire than when independent? Hammerfell held their own during the war when the Empire cut them loose. "The resistance is still strong in Hammerfell" tells me that it might be possible for an independent country to fight the Thalmor off. But can Skyrim do the same?
Like Hammerfell, Skyrim has a hostile environment which the locals know like the backs of their hands which would cause problems with a large invasion force. But the Thalmor in Skyrim may already be planning routes and such. (Unless Thalmor spies are ousted from Skyrim by Ulfric if he wins) Skyrim is also home to a race of ape-s*** barbarians who may well be the best Human warriors in Tamriel. Then again, the Redguards are also incredible warriors.
I personally think that the Empire wants Skyrim just for more Men to fight for Cyrodiil. While this would make sense to anyone, it also shows that the Empire would probably not return the favour. (Except with Legionnaires stationed in Skyrim)
The Empire could just say "We need warriors! Send us Nords!" But if Skyrim is attacked... "Cyrodiil is too weak to aid you. Besides, you have a good enough army, right?" This would weaken both Skyrim's armies and also the ties between the provinces.
So... could Skyrim fight the Thalmor alone?
P.S. I personally think that they'll still call on the other provinces for alliances. It would be stupid to not do so.