Hi. This is a wonderful plugin since it has helped us to manage several small networks more easily.
However we found an unexpected error, trying to activate some themes we weren't aware they were disabled, and i realized that just until reading the plugin code seeing it lists even network disabled themes to super admins, through the function "all the themes".
I'd suggest disabling the function, since it doesn't makes sense to having disabled themes listed if you can't activate it or preview on customize screen.
Another approach comes to my mind, but I don't know which function could be used to know if a theme is not enabled for the network/site. I've seen on this ticket a discussion on the "Cheatin' uh?" error "messages", and how to making them more informative.