Oh right, an instance doesn't work since the NavigationService wants to create the instance itself.
You could have the Frame created in your MainView and navigate from there if you need the navigation and then you can use
var mainView = _mefContainer.GetExport<MainView>();Window.Current.Content = mainView; Window.Current.Activate();
You're still stuck with pages not being pulled from a container, however, for navigation after MainView is loaded.
I think with the default navigation being view-first, you'll have to create your own navigation to use with MEF or move to a viewmodel first approach.
Caliburn.Micro fits in nicely if you're going that route. You'll have to pull the latest source as there hasn't been a release of the Win8 changes yet.