Since this is like the old floppy disk days, where any disk could be infected, would a version of the same solution apply? I'm thinking of the old boot-sector protectors that would announce your disk is clean, thereby occupying the space a virus would otherwise claim. Of course there would have to be something in place to verify this wasn't just malware calling itself a protector.
What this requires is called remote attestation. People have been working on this for smart cards and embedded systems, though PCs and VMs/cloud get more attention. It is very complex though.
