If they have permissions to delete a folder, that means they can delete its subfolders as well, which means they can delete any folder and there isn't a good way to control this behavior.
As an admin, I focus on a different approach. I only allow creation of folders using templates with pre-configured folder settings. Allowing deleting of folders then becomes a non-issue.
Otherwise, PDM will become a junkyard of folders that have to be cleaned up later. In my experience, if an admin allows them to create random folders that later aren't needed, the average user won't clean them up.
Every customer deals with this at one level or another so come to your own conclusions.