Whether he's intentionally helping them or not, its still obvious that the Thalmor think he's serving their purposes. All though, if I remember his dossier correctly, I don't think they actually intended him to start a full-fledged Civil War.
Or maybe they didn't want him to win.
They don't, because they know that if he does they're next on his hit-list. He even says so at the end of the Stormcloak quest line, although he couches it in terms such as 'leading the Empire to victory' and so on.
I typically support the Stormcloaks on those characters that actually bother with the whole mess, because the Empire has descended to a point where short-term survival is considered more important than maintenance of the alliances that will enable it to survive in the long term. As a result, supporting it is basically wasted effort as it's going to die sooner or later anyway and be replaced by a new entity.
What a lot of those who claim the WGC was necessary are forgetting is that the Thalmor army had just been obliterated, which implies that the Imperial army could have just kept on going and rolled them right up. I liken the situation to that of McClellan vs. Lee during the American Civil War: McClellan had Lee trapped, and beaten badly, but sat in his fortifications while Lee got away, rather than attacking and ending the war less than a year after it had started. McClellan, much like Titus Mede, had the bad habit of grossly overestimating the enemy's strength, and it cost him (and his nation) dearly.
Granted, we don't know whether or not the Thalmor actually had more forces or not, but based on accounts from both sides it seems pretty clear they didn't, or at least none that was close enough to intervene in time, save what was left of the army they'd sent to Hammerfell. Whether they did or not, though, the Empire should not have signed the WGC given the terms therein, as they
had to know that doing so would alienate the remaining provinces, which they could ill afford. Sure enough, doing so provoked the Civil War with Skyrim, as they saw the signing as rank betrayal, which resulted in the current situation.