A variety of solutions exist for refurbishing cones and races.
Removing rust marks or similar type staining is easy. all you have to do is find a creative to polish the questionable pieces. I polish axle cones on my buffing wheel and polish hub cups with a buffing pit on my Dremel or reuglar drill.
Anything more than surface contaimination CANNOT be fixed by polishing. Any pitting or cracks must be adressed differently. Back in the old days some of the guys would mount their cones in a lathe and cut them down until a smooth surface was present. As others previously mentioned this isnt a good idea becasue your maching away the hardened surface, it only works if the cone is harded all the way through. The best course of action is to find a new cone. Hub races are a different story. I recently had one with very severe rust damage that couldnt be polished out. I replaced the race with one from a hub with a damged shell.