Networkwide Plugins deactivated on main site?

Is there a plugin or strategy to activate plugins for the whole network, but having them not activated on the main site of a multiuser network?

For example I want to use plugins that do not have to be configurated or are simple to configurate for my customers, but on the main site I want to have them deactivated so that I can use there pro versions of some of the plugins or totally other plugins for the same work.

When I have the plugins for the customers and for the main site at the same time active it comes to conflicts.

And No I do not want to activate the plugins for the customers manually on each blog.

who has an idea how I can manage this?