I agree with tan. If you are using the same size rotors and calipers, I don't see how they can claim that the rotors caused a failure in the ABS system.
If you went in there and asked them to replace the rotors, I could understand. But if the ABS system is faulty, what rotors you have on the car wouldn't really make a difference. Again, they have to prove that any aftermarket part was the cause of the failure.
Sometimes it takes a call to SOA to straighten it out. Talk to the service manager, and if he can't help you, ask to get in touch with a SOA rep.