It will be worth less if the paint doesn't match front to rear. It's been in a collision, it's not going to have full value no matter what, so get the whole thing painted and it will look better. If it's painted properly it shouldn't be noticeable, get the body shop to paint the door jambs. If you're really anal, take off the seam trim and the door panels so they can paint all the way over to where it can't be seen (when the trim is reinstalled)..
I think that if it's black, it won't be noticeable anyway. If they're just going to paint the outside (not the door jambs), you could also blend the edge where old paint meets new paint with some cutting compound.