Well, if you're open to a philosophical change, I think the other way it could be handled is to actually change it to work in an additive way, using visual cues. I'm thinking that in page and module settings, it could show the Administrators role as always checked and grayed out (indicating that admins always have access), and content administrators as always checked by default but not grayed out (so the user can just uncheck content administrators to prevent them having access at that level).
If it were implemented this way then gurus would need to unlearn the old way of doing it, but I think it would be a lot more obvious what was going on for less experienced admins, and the checkboxes would really work the same for all of the roles.
Jamie