I use 00 or 0000 steel wool as a final step (sometimes even a fine wire brush) when I rust blue. As long as you don't rub the heck out of it, it won't hurt the finish at all. I have also used 0000 to clean up surface rust on old guns without harming the finish. I believe that the trick is to use fresh steel wool, turn it, change it, whatever it takes to avoid rubbing the loose crud around. The same thing applies if you use rags, burlap or whatever: If the rag gets built up with loose rust particles and you keep rubbing it around, it will act as an abrasive and you might damage the finish.
When I clean the rust off of an old gun, I soak it in Kroil and scrape off any rust scale with a broken piece of plexiglass (nice and sharp, but won't leave scratches). I prefer to polish it after it's clean and dry, as it keeps the gunk from accumulating in the steel wool. The brass wool might be a bit more gentle, but steel wool works fine for me and is way easier to find.
Here's a gun I cleaned up a while back, it had a light surface rust all over but I couldn't see any damage to the finish after polishing gently with 0000 steel wool (the edge wear was already there):
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