I re-read you question and understand it better.
Here is what you need to do...
Take the rotors off and clean all the rust off with some emery pad. doesnt need to be perfect.
Go and get some Rustolium BBQ Paint. This stuff is high heat and will grab very well. Paint the entire rotor front and back with a couple coats. I would do like 3. Do not tape off any area of the rotor. Paint everything.
When you go to brake the first time it will take off the paint where the brake pad touches, but leave everything else painted.