It seems as if there's a few mods out there that increase legion assassin spawn rates as some people have issues never seeing them. I on the other hand have never had this problem and after having killed them hundreds of times I've gotten a bit sick of it. I suppose you could just disable them completely but I think it would be better to somehow have a quest that leads to them no longer attacking you. Seeing how I have killed every single legion troop in the game other then the respawning ones it seems like they should really just give up.

You could become friendly with the legion.

Not if they are all dead sadly.

Alas, unless it was before the amnesty point after killing Benny, the hit put out on you by the Legion is permanent.