I had an issue similar to this during the civil war quest (Spoilers). Upon attacking Solitude and taking care of Tullius, when I went to out to listen to Ulfric's speech, the Stormcloaks ran up, saying, "You've commited crimes against Skyrim, what do you have to say?" I tried several different ways to get out of it, since I was in the middle of a mission, having to reload several times. Paying my bounty still triggered them to attack, bribes didn't work, etc. Finally I said "I submit, take me to jail" and immediately exited dialogue, and ran away from them. They didn't chase, I didn't go to jail, and everything seemed cool between us from then on. Not sure if this will work for you, but it's worth a shot.