I accidently killed a main quest NPC right after the caravan crew got wiped out. I've read that lots of others have done it too but now I can't do any quests at all!

I am wondering if there is any way to restart the DLC over and if not believe there should be a patch to allow people to do so, because it wasn't made blatantly obvious to most people that you weren't suppposed to shoot back.

Yeah, you have to reload a previous save. If you have only one save file, made after killing Follows-Chalk, there's no going back and you'll have to kill the important NPC's in the DLC.