There's really not much you can do. I assume that you still have the OE rotors, which resist corrosion better than anything else, believe it or not. Where is the rust; on the edges or where the pads actually contact? In the center hub section? Remember, rotors are basically just bare steel, and can rust even while washing your car.
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Adam Smittkamp
ACS Automotive Service, Inc.
*Your ACDelco Headquarters*