realized that the I/O pins cannot take more than 5.5V in or else they burn out...Actually
, the max input on a "Due" is 3.3Vhttp://arduino.cc/en/Main/ArduinoBoardDue#.Uxyrwz9dU8q
"Warning: Unlike other Arduino boards, the Arduino Due board runs at 3.3V. The maximum voltage that the I/O pins can tolerate is 3.3V. Providing higher voltages, like 5V to an I/O pin could damage the board."
Maybe it's salvageable still, depending which pin got the 12V.
You may have gotten away with only stuffing the programming port USB-TTL interface.
It may programmable via the ICSP.