Looks like a slick mod to the Arduino - What ISP do you tell AVRDude you are using?
I could see making a cable that when plugged in puts the 8U2 in ISP mode and when removed it works in normal Arduino mode.A 10 pin connector on the one end witht he 2 pins shorted. A six pin connector on the other end.
This might be a good addition to the Arduino design. And it could be used without having to load a sketch in your Arduino chip.
Will you post your code and the procedure for loading it in the 8U2?