Let me make sure I understand what you're trying to do:
You want a user to be able to edit *everything* about your site -- such as the site's name, enrollment policies, security settings, path variables, and so on (up to and including creating roles and assigning permissions to those roles) -- *except* for current courses? Even if you could mess around with the site administrator's permissions, I would question the wisdom of having more than one site admin anyway.
You might have to assign some users to an "editing teacher" role in courses that have not yet gone live, then remove that role from the user in that course when you make that course live. It's a more complicated way of doing things than you wanted, but it's probably a sounder approach.