Remove access to people who try to use /tool, /none, or /tool none. Make this command only available to people who have permission to use world-edit, because it's just a useless command for everyone else. It's completely harmless for anyone to type this, but I don't see why people can in the first place. Just a simple "You do not have access to this command" will do. Spoiler
This isn't relevant at all, though. In fact it's so irrelevant it doesn't even look like worldedit has a permission for this.
http://wiki.sk89q.com/wiki/WorldEdit/Reference EDIT: Realized that permissions and the actual command are different things. Still I don't see why it shouldn't be disabled... it's a useless command (or at least for users who can't use it even if worldedit had permissions).
Why does it matter? There's no permission for it because there's no need for one. It does nothing unless you have permissions for any of the other tool commands. adding a separate permission for it is pretty counter-intuitive. I don't see the problem here.