You can clean up the pins, you should take out the bushings/liners that remain in the hinge that is attached to the Jeep not the door. There is a good thread with photos and suggestions of where to order from http://www.wranglerforum.com/f202/door-hinge-bushing-fit-1206433.html
Once you clean them throw some white lithium grease on the pins, should keep them from rusting.
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