Currently restrictions are disabled. That means any applications that org members connect to their account have access to MeB repos and there's no way to disable that. There's also no way to give access to personal private repos without giving access to private ones under the MeB account.

See https://help.github.com/articles/about-third-party-application-restrictions/ for more info. And https://github.com/organizations/metabrainz/settings/oauth_application_policy.