The entire idea behind the program is BMW standing behind their quality parts. If their parts are rusting, that should be more of a reason for them to replace t hem under their program than less.
In short, that's an obnoxious statement. You have the program, and your brakes are covered. The corrosion should actually bring into question whether there's more work to be done rather than just pads and rotors. I'd tell them you're getting a third party shop to also check out the calipers and the rest of the suspension system. I'd be surprised if you don't need new struts and shocks too at that mileage.