There is a rust converting primer on the market that comes in a spray can. It converts light rust into an inert black oxide that protects the metal from further rust. Using an extension tube, you should be able to spray it into most of the areas of your main tubes and BB shell pretty well. Just mask the outside paint well to protect it from overspray. Online you can get it from Eastwood company with the extension tubing for coating the inside of vehicle frames.
http://www.eastwood.com/eastwood-rust-converter.html