If I understand your case correctly you have two categories of users: A has full access to all courses, B has full access to some courses?
In that case you can create two hidden courses:
- course A: its only purpose is to adminster the enrollment of category A participants,
- course B: its only purpose is to adminster the enrollment of category B participants.
Now all your regular courses can be meta-courses: some are fed by the course A participants only, other are fed by both course A and course B participants.
Afterthought: I realise I'm not sure about the changes in the meta-course mechanism in 1.7.