In WordPress MU, you can set a 'home' theme that can only be used by the main site but not network sites.
example.com can use 'home' theme (or whatever)
other.example.com can use the activated themes but not the 'home' theme.
I can't see a way to install a theme that can only be used by the main site. The main 'superadmin' could be able to select any theme even disabled ones or is there another solution.
On WordPress.com I don't think a user can select the theme that drives the homepage of wordpress.com for example, but I don't see how to do this with 3.0 beta2