You're missing the point. This is a military system. We cannot change the software easily (as in at all really).
Virus defenitions are still being provided by the DoD. EOL according to Symantec is not a concern.
At BEST I may be able to get SAV 10 on the XP systems, but 2000 are still running 9 and will do so until the EOL of the 'system' itself which may be 2012-2015.
The only problem I have is that I cannot call the scan from my application. There is a 3rd party tool called vpscan.exe which seems to be able to start scans. Unfortunatley using it as a means of starting scan isn't an ideal option as that's another .exe to get authorized for the system. Yet the fact that it exists clearly indicates that there is a way of starting scans - I just don't know what it is.