Okay, this is my theory on the whole subject... Feel free to debate this in a civillised maner...
The Thalmor, during the great war captured Ulfric, interrogated him, found out he was the son of a Jarl and released him after learning of his strong faith of Talos and his Defiant nature. Knowing he was going to reach a position of some power in the near future.
After the War, the Thalmor forced the defeated Empire to sign the White-Gold Concordat which as we all know, outlaws the worship of Talos. And knowing full well of what they learned from Ulfric that he would voice the strongest objections and plan a rebellion. So far so good. Ulfric becomes a Jarl and begins the construction of the Stormcloak Rebellion.
Ulfric kills King Toyrrg, forcing the Empire to place Skyrim under Martial law untill Ulfric is caught, tried and executed. Knowing that many Imperial soldiers will die hunting for him therefore weakening the already weak Empire. Eventually they capture Ulfric and he's about to be beheaded. However, Alduin shows up, an unexpected factor, Ulfric is free and ready to launch his all out civil war. This is good for the Thalmor because a civil war will weaken the Empire even further (when I say weaken, I don't just mean reducing their numbers, I mean weakening their morale also). But, they still expect the Empire to win the war.
Okay, at this point, lets say you the player choose to fight with the Stormcloaks...
The Stormcloaks win the war. What do the Thalmor have? Nothing they wanted. If the Empire had won, they'd still have some degree of control over Skyrim through the Empire. However, all they have is a loose cannon on the deck, unpredictable and in command of a bunch of savage warriors who would rather die than give up their man-god. Now the Thalmor have a problem. They can't fight the Stormcloaks effectively on Nord turf because of the rugged terrain, the cold weather, giants, dragons and some man or woman with a magic power far greater thant their own, running about the place slaying every Thalmor Justiciar in sight, rallying Nords all over the province to arms.
By choosing the Empire, you keep the chain of events flowing in favor of the Thalmor, who will eventually stab you in the back. Choose the Stormcloaks, you shatter that chain and force the Thalmor to re-think their strategy, and while they're doing that. Ulfric creates a United Front, possibly signs an alliance with Hammerfell and generally making themselves ready for war with the Thalmor.
In my opinion, the Stormcloaks do the most damage to the Thalmor, whilst aiding the Empire helps their plans come to fruitition...
