100% of the system is read only? I assume you are using a ramdrive or something like that for tmp files and the like? I don't know shit about windows, but I don't think it's going to run without any kind of writable space.
OTOH, if you want a simple solution to this issue, and the system is read-only, I think your simplest antivirus solution is called "reboot".
Of course, you should be looking into running GNU/Linux in this babies. It certainly runs better on Atom than windows ever will.
The flash drive is a read only maintenance tool. The system is not read only. He wants something that he can run from the flash drive.