I just did a rotor replacement on two Fords and the replacement rotors should not have rust on the inner cooling surface. You do have to clean the new rotors to remove the organic material used for rust protection.
Having turned rotors in the past, used and turned rotors usualyy have rust in the center section and hub (if not metal plated) while new rotors should have no rust at all.
I would complain to the service manager...
