You aren't going to hurt anything by hand polishing a stainless gun. I've done it a few times and have seen some outstanding results here on TFL, some guys work hard to get a real mirror-like finish.
I would stick with anything you can see when the cylinder is closed, but remove the cylinder and cylinder latch to make it easier. I like to use Mothers Mag and Aluminum Polish and soft cloths.
http://www.mothers.com/02_products/05100-05101.html