I think this sort of mod would only be logical after you finish the bulk of the vanilla game, as I have. Maybe it'd be possible to make all Thalmor outside cities to be hostile? Inside they'd have diplomatic immunity, you could say. But outside they'd be fair game for any highway bandit or, er, angry Dragonborn who they might come across.
I don't know, I haven't looked at all the factions for them. There might be a separate faction to which free-roaming Thalmor belong that does not include NPCs like Ancano, Elenwen, Ondelamar, etc.
However much it might improve gameplay, though, I'm not sure it would be very realistic, to be openly and immediately hostile to a citizen "just because" really isn't the Thalmor's style. If they have a reason to target a certain individual, yes, but when they are out to get the player they send designated hit squads after him/her and hope that it can be taken care of in a relatively quiet manner... and the ones giving the orders make it clear that the hit squads will be disavowed by their superiors if caught. Having them be hostile to you by default under all circumstances, even in the presense of witnesses who would otherwise be their allies, doesn't fit their style at all.