I recently traded in two of my guitars (a samick acoustic and a peavey electric) for an Epiphone Les Paul Special Model II and the bridge pickups are slightly rusted.
is there anyway to clean that up without damaging the pickups?
Rust is a chemical reaction, you can't 'clean it up'. Does it matter to you much? Because rusty pickups won't affect your sound...

Gibson Les Paul Custom (Ebony)
USA Jackson KV2 Sunburst
Jackson KE7
BC Rich NJ Classic Mockingbird

Marshall JVM410H
Marshall 1960A

Korg Pitchblack
MXR Super Comp
Dunlop Slash Wah
ISP Decimator
yes you can clean up rust, its a chemical reaction, but only on the surface! you can use steel wool to clean it up, but if they are rusting then they are probably not very high quality anyways so you might just want to replace them.
Well Enough Alone
alright, i know it doesn't affect sound. i just think it looks tacky.
steel wool? alrighty, thanks man.
actually steel wool might be a bad idea if you let the little pieces of steel get sucked inside the pickups... a better thing to try would be some organic cleaning stuff, like "simple green" and use a cotton swab to wipe off the rust.
Well Enough Alone
i have a fender p bass, i bought it used and everthing was rusted, tuning pegs, pickups, bridge, etc.... and i used steel wool to get it all off, and using steel wool to get off the rust will not effect the sound. If it does it would be because the rust is interfering with the pickups ability to pickup the sound from the strings