No, this does not work as of now.
If user 'John' is a member of an Organization and has permission to create a vApp/VM, he can create it in any Org-vDC which has available resources.
If you need separation, here are some options:
1. blocking tasks to confirm to some policy/process
2. use two different Organizations ... to which John doesn't have access to one of them.
3. Make your own portal to abstract information away from the user to not have the choice.
