A2 and A3 are clamped to within 0.15V of IOREF by the schottky diodes.
The only issue with the board is that the Brake lines are not guaranteed to work. Looking at the datasheet for the xnor chip: when the VDD is 5V, there is no specification of the output if you try to use 3.3V as a logic high input. However, the internal design of the chip very strongly suggests that it will simply do the right thing. Worst case: you live without the brakes, but no damage to the Due or shield.
Edit: No need to disable the current sensing pins. They already have a maximum output of 3.3V according to the product page, apparently for this very reason.