Try using some sort of calming spell or something, perhaps. Maybe mess around with some console commands, kill/resurrect, disable then re-enable him.
It can indeed get quite annoying when some characters want to kill you. Ulfric recently starting attacking me in the Solitude battle and wouldn't stop at all, fortunately continuing the quest made him give up, although the battle music wouldn't stop playing afterwards.
If you pissed him by friendly fire, I believe there are some mods which makes people never get mad about that. --- PSN: TheUndying84