Consider another instance of the problem: verifying that your webcam isn't being used to spy on you. Since a surprising number of hardware designers were negligent and made that software controllable it is orders of magnitude easier to simply deploy a piece of tape than try to prove that malware hasn't disabled the status LED:
http://security.stackexchange.com/questions/6758/can-webcams... http://blog.erratasec.com/2013/12/how-to-disable-webcam-ligh...
How much skill and diligence does it take to confirm that you have disabled the controller using each manufacturer's interface (if they even have one documented), that there isn't some way to re-enable it later (or that something like a sleep/resume cycle didn't reset the controller), and that all of that continues to be true for every subsequent configuration change or software/firmware update?
I would suggest that any organization with this level of risk would be better off paying someone $15/hour to check the ports along with the rest of their physical status checks and put the security engineers in charge of other improvements with a higher return.
If you are paranoid enough or have actual reason to believe somebody would want to invade your network, epoxy is one way you can be really certain no one can hijack your network via an infected USB flash drive.
EDIT: Of course, if gluing the USB ports shut is all you do stop attackers, I am pretty much begging for trouble. And as somebody pointed out, disconnecting the USB ports from the main board, possibly disabling the pins is probably a better idea, as well as disabling the USB controller in firmware and locking the BIOS / setup, if it is part of a ... let's say comprehensive approach to securing your network.