You've got a solid plugin here & I really appreciate what you've done with it. I've been making a minor change to it when I upgrade since 1.0 to let my site admins see their sites while they are in maintenance mode. All I'm doing is changing line 122 from
if (is_super_admin()) return;
if (is_super_admin()) || current_user_can('manage_options')) return;
Not sure if that is something you'd want in the plugin or not, but I thought I'd pass it along if it'll help.