Another option that would be a little messier - remove the pullups to 5V on the Mega, and add external pullups to 3.3V.
RN1 pins 2 & 3. Remove the part altogether, or cut the traces on the board going to pads 2 & 3. RN1 is the 8-pin part inside of D30 on the dual row header on a Mega Rev3.
