I was enrolled in the anti-paladin extermination quest, and so, when looking at the anti-paladins in the bridge district, they immediately began to fight some smugglers. (I am not sure if this has happened to me before) and I decided to kill them all, without talking to them. Now I am stuck with the guy in the order saying he is waiting. Is there any other paladin quests or a away to get around this, as I have no save from about that time.

If every one is dead, then the quest has been failed. You were supposed to try to keep the fallen paladins alive for a while.

With the emphasis on the 'for a while' ;)