I killed Halvard as part of the DB questline and had no problem (well that is a lie, I had a radiant quest open and had to finish it before the Jarl would give me the get him a drink quest).
Neither the Jarl nor the new steward ever seemed angry at me or hateful towards me...
Question for those of you having problems because you killed Halvard: Did someone see you do it? I always made sure no one saw me kill anyone in the DB quests. Maybe that makes a difference.
For the Imperium!
Thanks to Gackt for the sig