The only idea I could have (but not experimented and I don't know if this possible) is that you add a "hidden" field to the users (I think it is possible to add fields - not sure).
If this is possible to add a hidden field, you could use the JMS plugin "multisites ID" that you can download for free.
www.jms2win.com/free-download
This "Multisites ID" plugin can be used to fill any values in a form or whatever and replace a pattern with the JMS "site ID".
If you put a special default value in your "hidden" field, you could fill it dynamically with the plugin and set the appropriate Site ID that will be associated to the users.
Once you will have this site ID associated to the user, you will have to modify the Community Builder to filter correctly the users based on the additional field.
Develop such behavior will probably require several days of work.
If you want that we investigate a solution for you, I suggest that you order our billable support at
www.jms2win.com/download?page=shop.produ...35&category_id=1
We already proceed like that for some customer for whom we have developped specific "modified" extension to filter information.