In order to track student use of the messaging feature, students could have a dropdown box to select the class that the message pertains to.  Only after selecting a class would the text pane show up to allow them to send a message.  Maybe the student roster could appear for them to select recipients.  Then a teacher can view the use of messaging to ensure it is appropriate and on task.  If a student abuses the privilege, then the feature for that particular user can be turned off.