As NukEvil says:

Flash drives/other removable media have nothing to do with their current problem.Stupidity seems to be the major issue. Another issue is a lack of adherence to policies (if they even have any) regarding basic system protection (weak/blank passwords, etc)...
This is a much more fundamental and deep seated problem that has nothing to do with technology or operating systems. In fact, to suggest that it has is to make an even greater mistake of suggesting that technology can provide the solution. Which, of itself, it cannot.

This is about:

1. A security model.
2. Security policies.
3. Security processes to enforce the policies.
4. Security procedures to support the processes.
5. Governance & management of the security system.

Given that there is generally a high turnover of personel in military and government environments it is vital that there is an appropriate succession and training mechanism to prevent the whole system being gradually degraded.