Why is my SUV making a high-pitched squeaking when I brake?

More than likly the noise is coming from the area where the brake pad meets the rotor. The old pads have been worn in in certain direction and now have a "cut" on them that would be the same as the worn rotor you had taken off. The noise may go away after some miles of driving as the pad wears to fit the new rotor. Also it could be the brake pad material does not match the the brake rotor material. Brakes are now made to be a match set in alot of cases. The pad material will embed into the rotor. This keeps the brakes quite and keeps the brakes cooler and last longer. An inspection of the brakes would be needed to determine if there is a safety issue with the brakes