Hi Yaemish,
Could you describe more about what you expect users to do with containers, and what restrictions you'd like to put on them?
Are you trying to control who can run and configure the containers themselves, or are you trying to control who can access the containers at all?
Controlling who can configure and run containers could be done by proxying the Docker daemon's remote API and adding authentication and authorization to that proxy. Controlling access to individual containers is trickier and it would help if I understood what you wanted to control.
Typically I don't think of containers as something users have accounts "in", and so the idea of needing to manage a lot of user groups is pretty foreign to me.
/Andy