Remove the ATmega328. If you can reprogram the ATmega8u2 then the rest of the board is salvageable.
If you're using the standard jumper wires with male pin on the end to make connections to the board headers, you might take a bunch of them, cut them in half, and solder a small value resistorin the leads, 220 to 330 ohms. Put some tape or tubing over the connections to isolate the bareconnections. Goes a long way towards protecting I/O pins from overvoltage and short-circuits.
I'll keep that in mind. I just happened to make a dumb wiring mistake.