I just created a new user class "alien". I added a registered user to that class but he can still access the forums etc. I went to "menus" and changed visibility to "members" but that doesn't solve the issue. I'm guessing that the newly created user class is higher in status than the default registered user.
Also, is there a way to somehow "deactivate" or "suspend" a registered user and still keep their account in the system for future reactivation?
The userclass 'members' includes every single user on your installation regardless of other userclasses that are set. I don't think you can set auser to inactive, you'd have to play around with the permissions and userclasses.
In e107 2.0 you'll find that the userclasses have had loads of attention as they use an hierarchical structure. This way, achieving what you want is simplified.