There was nothing wrong with Grand Zero's explanation of organ donation. The problem was with his translation of "brain-dead" into computer terms. Since we have CPU hardware, short-term data storage, and long-term data storage all in one irreplaceable unit, it's hard for us to remember that the important part is the data, not the hardware.
The situation is this (correct me if I'm wrong): The EU probe is missing one crucial part (the CPU) which could be replaced. If it were replaced, the probe would be good as new, with all memories and personality (such as it was) intact.
Andrew has all his physical parts (except the thermocouple, which evidently isn't absolutely required). He's missing data, which is pretty much irreplaceable. His short-term is all gone, and a substantial part of his long-term is gone. We could replace the software -- the operating system and so forth -- and get him going again, but the data (memories and personality) is pretty much gone. He'd be a newborn probe, not our Andrew.
Now, what we want is an ethical/moral argument that allows us to cannibalize the repairable EU probe and use the parts in the brain-dead Andrew to get a newborn Alpha probe. I'm having trouble coming up with one.
(It's interesting that the probes initially seemed to have the same problem with perspective that we do. Gail's description of her attack on the EU probe, and her mental state since then, certainly led us to believe that the EU probe's situation was at least as serious as Andrew's.)
-Erin