Too bad there is no mod that makes her a playable follower. If Skyrim has incorporated some of the schematics from Dragon Age, Elenwen would certainly be a follower. It would be strange how she would "join" the Dragonborn, but clearly that would be based on how you progress in the story.
As for a reason for how that could be lore friendly, the Thalmor have no interest in fighting the empire. They merely did so on behalf of their Wood Elf Brothers who were being attacked by the Empire in Valenwood. The Thalmor, like all high elves prefer to being in power than out of power, but as such intelligent beings they are not prone towards violence and thus prefer using diplomacy as would the imperials of cyrodiil as to avoid bloodshed.
Why the altmer Thalmor would thus not be able to coop under imperial rule has to do with the sin of pride, which the thalmor reek.
Thus Elenwen preferring to gain control over the Nords as a means to weaken the empire to thus diplomatically claiming hegemony over all of tamriel would probably accompany the Dragonborn for that very reason. Gain the trust of the Nords by vanquishing the dragons, also insuring the dragons don't become a menace to the Aldmeri Dominion and as a result destroy the StormCloaks (who hate the Thalmor) and weaken the Empire till it is absorbed into the Aldmeri Dominion diplomatically.
According to Ulfric's Dossier, she had been his interrogater and, as follows, perhaps tortured him during the Great War. Probably explains his aversion to her at the optional Council at High Hrothgar. In any event, she is an essential that cannot be killed, I believe, and like as not will have a bigger role in the story.
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As for a reason for how that could be lore friendly, the Thalmor have no interest in fighting the empire. They merely did so on behalf of their Wood Elf Brothers who were being attacked by the Empire in Valenwood. The Thalmor, like all high elves prefer to being in power than out of power, but as such intelligent beings they are not prone towards violence and thus prefer using diplomacy as would the imperials of cyrodiil as to avoid bloodshed.
Why the altmer Thalmor would thus not be able to coop under imperial rule has to do with the sin of pride, which the thalmor reek.
Thus Elenwen preferring to gain control over the Nords as a means to weaken the empire to thus diplomatically claiming hegemony over all of tamriel would probably accompany the Dragonborn for that very reason. Gain the trust of the Nords by vanquishing the dragons, also insuring the dragons don't become a menace to the Aldmeri Dominion and as a result destroy the StormCloaks (who hate the Thalmor) and weaken the Empire till it is absorbed into the Aldmeri Dominion diplomatically.