Don't wipe out the Aedui, transplant them somewhere else. If you're savvy with the move_character command and have Force Diplomacy installed, transplant them to Galatia (currently held by Pontos according to your campaign map) or Tylis (which looks rebel) or if you just want them out of the way, Ireland. Killing factions off is a waste, especially when they can become something else in another place.