what i did with my last car was clean it up good and clear coat the area of the rotor where the pad doesnt touch with high temp clear coat...it worked good. i also did it on my aeros welds on the exhaust...everything is all rust free still...
It's gonna be a few specs of overspray that the pads will remove without trouble. I'm not saying go crazy and paint the whole thing but think about how much debris the pads have to remove during normal everyday use that have been picked up by the discs. Far more than a few microns deep of paint I would assume.
I did exactly as Chris did and it seems to have worked great. The little bits of over spray disappeared after my first drive and I certainly don't think that the pads were ill affected.
I did wipe off as much overspray as possible from the rotors with a rag after each coat.