I'm late to the party and much of what I say here has been said by others in the thread - please just bear with me.
To my mind, the Thalmor would not prefer an Imperial victory for one of the most basic reasons: their apparent strategy of 'divide and conquer'. As has been pointed out in other threads, the Dominion, weakened though it has been with time and war, has taken deliberate steps to sow the seeds of discord and discontent among the provinces and the Imperial seat. Call me cynical, but it seems clear to me that the situation with Hammerfell was indeed something of a calculated maneuver to drive a wedge between that province and the Empire. I wouldn't be the least bit surprised if the Dominion executed a strategic withdrawal in that particular circumstance, after recognizing that what they sought had been achieved to their satisfaction. Do NOT get me wrong, I give the Redguards a great deal of credit for fighting so fiercely and bringing it all to a stalemate. I'll never begrudge them that. I just feel that if the pronounced chess-like mechanics were not involved, the stalemate would have gone on even longer or maybe have ended up quite differently. That's just my feeling, however.
In any case, the events in Skyrim are an echoing of the same tactics. A Skyrim torn apart by civil war naturally puts it in a much weaker position to directly oppose and battle the Dominion's forces. And the Thalmor/Dominion are well aware of this, as they allude to in their dossier. A quick, decisive victory on either side allows the civil bloodletting to be staunched at least for the present time - which of course is unfavorable to the Dominion. A long, drawn out conflict drains both blood and resources, and allows the Dominion to both reorganize and capitalize on the collective fatigue of their targets. A Stormcloak victory allows them an advantage of, well, vantage point. As well as time to bide. While the Empire would have to contend with a separated Skyrim, either letting it go or sending reinforcements to try to reverse the situation, the Dominion would have that time utterly at their disposal.
Hmm, tldr;
All in all, the Dominion needs time on their side. Because time yields the blood of those they seek to dominate, in Skyrim and throughout the Empire. As with Hammerfell, Skyrim is another point of focus for the deployment of deliberate strife and stress on its bonds with the Empire. It seems to me that as the Dominion has indeed been weakened overall, dividing and conquering by proxy - as it has been doing right along - is the greatest hope it has of dismantling the Empire and claiming the provinces. Of course much of this discussion is heavy with speculation. But it's one of the conclusions that drives me to play for the Empire. I despise the Thalmor as much as any Stormcloak and would love to see the Empire reinvigorated and able to finally put the Dominion types to rest. The Stormcloaks aren't the only ones who declare their intent to 'liberate' Skyrim. I believe Nords of the Legion like Hadvar and Rikke would strongly concur.
As Bulbaquil pointed out, even with an Imperial victory there is still evidence of a lingering rebellion, seen no less in the camps that continue to dot the countryside of Skyrim. During my post-war travels, I acknowledge both them and the resentment and even hatred in the voices of some Stormcloak sympathizers. It's something that will haunt the Empire no matter what happens. And that makes it all even more interesting to think about. Despite my own hypotheses, the twin ambiguity and complexity of the whole matter is clear to me. And rather striking.
also the empire is the thalmor's puppet so that's why 
