The easiest way would be to disable it in the BIOS settings. Other than that, compile a kernel without USB support as either a built-in or a module. With most Liniux distributions it may be possible to do this just by removing the relevant modules from /lib/modules.
Of course, anything that you do can easily be countermanded by someone with root access. Make sure that users don't have root access and that any sudo privileges are closely controlled.