If they're rusted, they've lost their plating. And they will rust again promptly upon reassembly. Best and easiest to simply replace them. From the looks of it, I'd consider replacing your studs too. Several look badly rusted and that will reduce their strength and stretch. You are likely to find that when you reassemble your top end and torque the nuts, that you shear one or more studs. Then you get to start all over again...
If you do opt to remove/replace your studs, use a stud puller and cinch it as close as possible to the deck. Heat the stud at the block until it's cherry red, rap the end of the stud with a dead blow, then twist it out carefully with the stud puller. Guaranteed to prevent shearing and snapping off of the existing stud.