I second Bill. Personally I prefer a light buffing with Flitz. Gives the barrel a more even polish, but either way, it's not a bullseye pistol so you shouldn't see much difference. Heck, it might actually shoot better. I would pay more attention to the crown than anything else.Just clean the rust out.
It's not likely to affect accuracy.
Run some wads of 0000 steel wool down the barrel.