Are you setting them as email-only from the start? When inviting new users, I would make sure that you go to advanced settings and set them as email-only. Otherwise, there is a 14day free trial where they have the ability to log into the system and get defaulted to full users. Sidenote: we have a new license type for clients coming out soon that will be free and provide much more functionality than email only users (ability to login, submit and view cases, easily collaborate on documents, etc.).
As for Super Users and licenses, I don't think we could do this even with a customization. They would have to be Admins unfortunately, which I would dole out very carefully.