I would hope both MT and DB would be present in the game as two guilds at war spices things up.
However, MT probably wouldn't be legal outside the Dunmer city so like DB, they would have to use stealth to kill (do remember that they were active through entire Tamriel and they probably weren't legal anywhere but in Morrowind either).
Also, I think I recently read somewhere in the Imperial Library how MT did act in Skyrim as well so it wouldn't be that weird for them to move their base there.