If you own/control the iPads that run iOS 6, you can turn off Messages via Apple Configurator or an MDM solution and the students would, to the best of my knowledge, not be able to turn that back on without knowing the Restrictions passcode. For personally owned iPads, the only way to block Messages would be to block the ports at your router. Messages uses port 5222, so if you block that port, that should block the transmission of messages, though the students will still try. For more information on ports, see:
Of course if the student has a cell connection on a personally-owned device, there won't be any way you can block the sending of messages at all.