PB Blaster, WD-40, try different size wrenches, vise grips, or pipe wrenches. Put some of those kitchen grip things on the nuts if you are worried about scratching anything. most people just take the nuts off and leave them off though.
i think you should probably just sell the jeep and get a honda. If you can't figure out how to get the doors off then there is no way your mind can wrap around any other situations that may arise from jeep ownership
Man that sucks.. only thing i can think of if you can't get a set of vise grips on the nuts the just cut the shaft just above the nut, its not serving any purpose if your not going to put nuts back on the doors, if you cant get to the shaft without hurting the paint to your rig, unbolt the hindges off the body, then remove the door and hinge, set it on your work bench and have at it.... one way we use to get stuck nuts off shafts is to get your cutting wheel, cut a slit in the nut all the way to the stud saft, then take a chisel and drive it into the slit, the nut will expand and come right off, I had to do that to my girlfriend's dad's YJ..
I personally always prefer to try and save the shaft. You may lose a nut in doing so, but you can get by without them. If you don't have a good shaft, well, it just won't ever sit right....
One thing you have to be careful of is turning the wrench the wrong way. Since the nut is on the bottom some people have been known to turn it the wrong way.