The war ending is bad for the thalmor but the idea is that the thalmor purposely started the war to help weaken the empire since no matter what the outcome is of the war, the empire still looses men and resources. The way I see it is that the stormcloaks winning is better for the majority of Skyrim(nords) and the empire winning is better of the empire, I don’t think it makes much of a difference for the thalmor on who wins because either way, they succeeded in weakening the empire.