looking at my 10.2.2 server, when I create a folder in AGS manager, it creates two physical folders on my D drive (but default is C drive), and at least one other on my c)
d:\arcgisserver\directories\arcgissystem\arcgisinput\myNewFolder
d:\arcgisserver\directories\arcgisoutput\myNewFolder
c:\arcgisserver\config-store\services\myNewFolder
I'm the admin and I don't have another non admin account to be able to see whether it would work or not, or what error they would get. Of course, best case, I would think you wouldnt even want them to see the folder exists. My guess, it will still be listed, but it would give them an error when trying to publish.
although this may work, I am no expert on what messing around with the folder permissions will do. Make sure you have a way to restore (backup, or how to reverse any folder permission changes) before you mess with things. I'm not sure that any of the above would be suggested by tech support....and it may be good to talk to them first.