A couple points:

- the link under Tools about deleting a site is not Super Admin specific. This is accessible to administrators of any sub-site.

- and in 3.1 all the super admin menu items will be moved to the Network Dashboard, which is a separate area. There is no mention of a super admin, actually (now that I'm combing over it). By release, the Super Admin menu page should have a notice at the top, probably not a full redirection for upgrade stragglers.