All past elder scrolls games, you could stop in the middle of the main quest and go off and do the expansion, then come back to the original main storyline and finish the game. I haven't finished Skyrim's mainquest (barely started it, been so busy with sidequests) so I am not sure whether some sort of "war with the Thalmor" could exist congruently with an unfinished main quest. I am trying to recall how Tribunal worked with Morrowind, I think finishing the expansion first meant an end to ashstorms, and that you could try to discuss the events with regular NPCs but they would get annoyed with you and think you were loony. Can't recall how Vivec in particular would respond to the news.
Anyway, I think it would have to be something that could be done alongside the main Skyrim quest without having one completely negate the other.
If a war with Thalmor would fit in there ok, then it sounds like a good DLC prediction. I am sure a lot of us are itching to have an excuse to kill a few more Thalmor. Interesting twist of course would be if you came to semi agree with them after learning more, just like the main game starts you thinking the Stormcloaks are the heroes then revising your opinion halfway through.
Tribunal expected players to of finished the main quest before playing the expansion - after all, the events in Tribunal are set to occur right after Morrowind's MQ completion.
However you could still start the Tribunal expansion right from the start of the game. Was rather bad of an oversight, and didn't work very well. Especailly since if you had Tribunal installed and started a new character you'd constantly be attacked by Dark Brotherhood assassins at level 1 for "no reason" (they are supposed to be attacking the person who finished the MQ though). The only way to stop the attacks (that were scaled to your level, sans the armor they wore) was to start the expansion - which was aimed at "high" 20-30 level players in difficulty.
Long story short it really didn't work. You pretty much need to install a mod that disables tribunal until after MQ or major faction completion or something in order to play Morrowind without going crazy.