From the WD-40 website:
“What surfaces or materials are OK to use WD-40 Multi-Use Product on?
WD-40 Multi-Use Product can be used on just about everything. It is safe to use on metal, rubber, wood and plastic. It can also be applied to painted metal surfaces without harming the paint. Polycarbonate and clear polystyrene plastic are among the few surfaces on which to avoid using a petroleum-based product like WD-40 Multi-Use Product.”
You’re going to repaint the car anyway, so it probably can’t hurt. But after sanding down to bare metal you may need to wipe down thoroughly with acetone or the like to remove any WD-40 residue before applying the primer.