It can definitely work to program it, but first the system needs two things - a bootloader on the processor and a program with which to upload the code that runs on your computer system.
It should be fairly simple implement, but it could use a volunteer to look into it. If you'd be interested in investigating, maybe we could make a resource area for it that could narrow down the things that need to be done to make it happen.
More information on bootloaders, and possibly easy code to modify for our needs:
http://hubbard.engr.scu.edu/embedded/avr/bootloader/index.html
http://projects.gbdt.com.au/boot162/
STKLOAD might be the answer to the question of how to upload on the pc side.
I like this page too, you kind of have to read it in a Pavel Chekov voice:
http://www.scienceprog.com/usb-bootloaders-for-avr-microcontrollers/
Regarding Arduino burning:
I've written up a short article that describes more about the arduino modification, I've been uploading code to my microdec via mine:
http://www.openmusiclabs.com/learning/arduino/isp/