I guess in case anyone else runs into the same problem as me, I should update this thread to tell how I fixed the printer.
I have already fixed the printer. Luckily the motherboard was not bricked.
I ended up buying a sparkfun AVR Pocket Programmer (about $15) and re-flashed the ATMEGA1280 over ICSP using AVRDUDE. It worked like a charm and the firmware took immediately.

If anyone has the same symptoms as me, your motherboard is probably not bricked. Fortunately, buying a simple AVR Programmer (like the sparkfun one) is cheaper than buying a new motherboard for the printer.
Special NOTE: just make sure that the programmer can handle the flash size of whatever chip is controlling your printer's motherboard (the sparkfun programmer just barely can do a flash size of 128 kb, the size of the ATMEGA1280's flash memory).