Brake pedal vibration under brake load is generally a sign of lateral runout on the rotors. Replacing the pads is not necessary, don't waste your money.
In general (and as stated in the CX-9 user guide Sect 4 - Pg 6) brakes shouldn't be used particularly aggressively during the first 600 miles (or after new pads/rotors), as this can cause rotors to warp.