Why not? If the supercomputer was pre-existing, the Other OS option won't disappear unless they do a firmware update. The only reason I know of to do an update is to play the latest games, so unless they're having sessions of GTA in between protein folding, I doubt it's an issue.
PS3 firmwares can now be downgraded. Somebody discovered a service dongle key, which allows for downgrading FWs (but not the latest). That would make it slightly easier to find replacements.
Also somebody is working on some patches which allow
linux to run on top of the same gameos hypervisor that the commercial games do. This allows access to an extra spu and
slightly more ram too. It does require an exploit to allow the execution of unsigned code. Here's the git repo:
http://git.marcansoft.com/?p=asbestos.git
Hector Martin has been playing with kinect for the past month so that explains the lack of progress.
I don't think this is a big issue if you're buying in bulk. With that many PS3's, you should have a good estimate of how many are going to fail in the lifetime of the supercomputer. I doubt the Air Force didn't buy spares already, since they don't want to rely on Sony building new PS3s.
