Of course they could just tag all authorised USB drives with RFID chips with unique ID codes matching the owners they are assigned to and their clearance levels, and equip their machines and the installations with RFID scanners designed to both detect the RFID and also to verify that the chip matches the drive being used.
If the USB doesn't have the RFID, or it doesn't match the carrier or it has the wrong clearance code or the drive doesn't match the RFID ...alarms, guns, trouble.
If the USB doesn't have the RFID, or it doesn't match the carrier or it has the wrong clearance code or the drive doesn't match the RFID ...alarms, guns, trouble.