This is a fairly common network security feature amongst companies (at least hospitals that I've worked in) and is now also DoD wide. If I stick anything into the USB port my computer is immediately locked out and the only way to unlock is to go in front of my Commanding Officer and explain why I was boneheaded enough to do so.
It stinks, it stinks even more in an educational setting; however, you find ways to deal with it. You end up emailing more, you end up using a network share drive more (if available, would be nice at KP), and you end up remembering what that CD writable drive is for.
I must say that no matter how much I hate this it actually is a huge security risk to allow thumb drives/external hard drives to a network. They are almost always manufactured in foreign countries (ie China) and who knows what those companies are putting in the background of the drives. The other issue is simply what people do with the drives. They put all sorts of internet downloaded and transferred files on them and rarely run a malware/virus scan on the things. Then there is the "hey look what I found" idea and the first instinct is to immediately insert it in the computer.
Now, my guess is that the IT dept will find a way to work with this and the midshipmen. The DoD has begun to allow some external drives back on; however, they have to be vetted by the IT's and can then not be connected to any computer outside the network.