Just as the title says.

I completed that bloodbath quest by killing all the Dunmer and got a bounty of over 5000, so I Divine Interventioned back the Moonmoth and ran to the quest-giver because he eliminates the bounty. The Legion was still chasing me when I talked to him, though. I'm also part of House Telvanni, the Tribunal Temple and the Ashlanders, which lowers disposition among the Imperial Legion, and the only faction with a positive modifier I'm part of is the Mages Guild.

So are they attacking me because of a bug involving that bloodbath quest, or because I'm part of too many of their enemy factions?

I think it's because your bounty was too high in the end. The way I've always done that quest was by taunting each person. It takes a long time, but is a lot less painful.

Naw, talking to the guy is supposed to kill any bounty you may have gotten, and the Hlaalu, Telvanni, etc. guards are all friendly, I've even talked to them.

I've seen other people report the same thing in the past. If the Legion members were already chasing you before you talked to Varro, they may have had their Fight levels raised high enough to attack you, which means that clearing your bounty won't help. Try selecting them with the console and typing setfight 30.

in that case, wouldn't going away for three or five cause the area to reset and thus causing the guards to forgot the crime?