I'm not sure I understand exactly what your issue is. Yes, when "Facebook User Only" is set in JFBConnect, we create a username like fb_12345 (where the number is actually your FB user ID). This is done, specifically so, like you say, there are no clashes.
How are you configuring your Community Builder, and JFBConnect, installations and how is the username being set to "John Smith". Is this during initial registration (using Facebook), or is this if a user has an account on your site already and is trying to 'connect' it to their Facebook account?
Sorry for the questions. There's been a few corner issues with CB lately that we're trying to wrap our heads around, but it's with specific configurations and can be difficult to duplicate. Any feedback you can give is much appreciated!