The only thing I can suggest that will work for you, would be to organize the students folders under a top level share folder. The top level share folders on the NAS can not be manipulated into Windows, however folders under the share folder can be. You could make a top level share folder named Students on the Buffalo, and then name a folder for each student using windows explorer and making folders under the Student folder. you will then be able to organize and delete the folders like you are asking about.
Unfortunately, this seems to be somewhat common in dedicated devices. I added an IP copier scanner, that allowed you to enter in users names and then specify what directory the scan would go to. I entered in the employees (about 50 of them) and then when I updated the firmware for the scanner, I found out the same thing that it organized the users by the order that they were entered. Luckily, the users havnt complained yet, but if they do that will be 2 hours or so that were wasted. Some times it just seems that not that much common sense goes into theses things.
Well I hope this helps. You should be able to do what you want to do like this, even though it is a bit of a work around.