I once worked for a company that wrote web banking software. The laptops/desktops/etc of certain employees had a 'driver' that continually monitored the USB ports. If anything plugged into it that had storage on it but not the proper corporate auth key to connect as an approved storage device? It would automatically send an email to the IT department, immediately shut off the entire USB subsystem in the OS, and it stayed that way until the device was re-imaged (in many cases making the device completely useless). It also got you immediately perp-walked out of the building and freshly unemployed, unless you could immediately give them a reasonable (and provable) explanation as to why it happened.
Now in this case, I suspect that if the bad stick presented itself to the OS as a keyboard/mouse/whatever, it may circumvent that (I say "may" because I don't know if it would be able to dump any non-keyboard/mouse-related data onto the machine w/o presenting itself as storage.)
Either way, if you're that worried about it, then epoxy the USB ports shut (well, except on the phone for obvious reasons...)