Prevent Directory Sync from disabling mailboxes in cloud when on-premise Exchange accounts enabled.

We are running Directory Sync (FIM 2010 R2) and also host on-premise Exchange accounts for our faculty and staff.  365 accounts are basically for students.  We have Directory Sync running and its running well but we would like the ability to turn off the disabling of mailboxes function on 365 part in directory sync.  Is there a way to configure the Windows Azure Active Directory Connector or Active Directory Connector to prevent it from disabling a mailbox on 365 and just skip it if the in-house AD object reverts changes to an in-house Exchange account.  I know we are not running a standard configuration, but there must be other schools or sites that allow for duplicate accounts and take this into account.  I would like to know how they handle these situations as well.