At this time the Messages app cannot be disabled or removed, at least not by any method I've been able to find. All you can do is block messages in your router, which could affect other, legitimate, use. It's certainly something that should be in the Restrictions; perhaps in the next iOS update. You can express your desire for such a feature to Apple via their feedback page:
You cannot remove any of the preinstalled apps. From what I see - you cannot restrict it either with restrictions.
Perhaps you should try to contact Apple directly for a solution.
I have read about people that bought iPads that were missing certain settings - iPads that were Purchased as demo models from retailers and their iPads did not have certain standard settings. There must be a way that you can disable those types of things from iPads being used in schools, otherwise, you could have chaos on your hands with apps like Message.
Perhaps you can look for an "iPads in the classroom" forums and see if you can get some direction from one of those.