I would say this is actually the reason why it doesn't make any sense for Google Apps to support Google+.
As you say, the core use case for Google Apps is for an enterprise, university, or some other kind of organization to give accounts to users that are managed on their behalf. In essence, all of the accounts are owned by the organization, not the user. Now, what happens when the organization revokes your account, because you graduate? The idea that that is possible is absurd.
(In case anyone reading doesn't see what I mean yet, imagine if Facebook locked you out of your account when your University cancelled your e-mail address after graduation, instead of just letting you associate a new one; your Google Apps account isn't just an account associated with an address at a domain, it is an account that is equivalent to an address at a domain.)
I have my own Apps account and was peeved at having to create another Google account for Google+, but now I'll continue to use a "personal" Google account for Plus. This way my Google+ will never be tied down to one organization (even if it happens to be my own at the moment).
They really need to decouple a Google account from a person's email address(s).
As you say, the core use case for Google Apps is for an enterprise, university, or some other kind of organization to give accounts to users that are managed on their behalf. In essence, all of the accounts are owned by the organization, not the user. Now, what happens when the organization revokes your account, because you graduate? The idea that that is possible is absurd.
(In case anyone reading doesn't see what I mean yet, imagine if Facebook locked you out of your account when your University cancelled your e-mail address after graduation, instead of just letting you associate a new one; your Google Apps account isn't just an account associated with an address at a domain, it is an account that is equivalent to an address at a domain.)