Once a pit starts it's never going to stop growing deeper.Might be okay to shoot forever like it is.
Myself I'd try and find a reputable smith to 'safely' hone them out or I'd sell it like it is.
I don't believe that at all. It's not bacteria, it's corrosion. A blackpowder gun may be a different animal due to the use of corrosive powder and difficulty in removing all the residue.
The ideas for removal of the oxides (rust) on the surface should help alleviate the porous rust from retaining moisture and continuing to rust, but my smokeless powder guns don't have that problem. If you were intent on removing the rust chemically, use the Brownells rust and blue remover liquid. Personally, I see no reason to do anything other than clean and oil as normal.