Getting another stock rod is cheap, just get a new one. Its not worth ruining a whole build over $50 worth of parts.
Im assuming its bad enough, because if you would want to "polish" it, then its more than likely too big a scratch to risk. By "polishing" enough to remove a considerable scratch you will remove a considerable amount of material and ruin the tolerances between the pin a rod and thats real bad. Even a small movement can result in destruction over time when dealing with the forces involved on that specific part.