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Never had a problem with them in any environment I've managed. As with most things governmental, the problem lies with a lack of preparation, and choosing to be reactionary rather than having safeguards in place to protect the system.
Most, if not all, antivirus applications have the option to scan removable media upon activation. One the drive mounts, the scanner will search the contents of the drive and alert you to any viral or other malware threats.
The disabling of auto run (a stig requirement) along with updated anti virus signatures is an extremely strong deterrent for thumb drive malware as 99% propagates via the auto run feature of windows.