Rust is usually caused by long term exposure of metal to water. You really shouldn't worry about wet sanding it as long as you dry it out thoroughly - and then use a rust inhibitor solvent.
Do your initial wet sand, trying not to go to bare metal. Rinse out cab and let dry. Use a rust inhibiting metal prep solvent, along with a wax and grease remover. Body fill/putty any scratches, sand and prime. Wet sand again, making sure you avoid sanding through the primer and body fill. Rinse out cab and let dry. Use a prep solvent again and spray your topcoat.
