Some times there is just a faction gliche, and hence the need for saves. As a matter of a fact, I just had a faction problem in one of the vanilla campaigns with my archer. When I returned to a merchant to get stocked up on heals, he was hostile. So were all the other merchants in the area later on.
'> I was forced to let my character get killed and then respawned to reset the factions. It worked fine except that the original merchant who went hostile was gone. I tried running away as soon as I noticed the gliche but when I clicked to talk to him, not noticing the color change (damn glaucoma!) I may have accidentally one-shot killed him.
I did have an earlier save available but decided it was just too tedious to redo all the events up to that point and just continued sans one merchant.
'> Several saves is the best strategy to avoid that problem but I get lazy.
NEVER NEVER kill neutral rats!
*insert image of cute fuzzy little innocent rat here*