Earlier this month, Microsoft announced that Office 365 will now support the ability to break Directory Synchronization if a customer chooses to do so.
Though through the Office 365 Admin page, when enabling Directory Synchronization it still gives the warning that if it is enabled it cannot be disabled, the fact is you can use the Office 365 Online PowerShell module allows you to connect to your environment and disable it.
In the past, if a user was brought over by Synchronization, that user was permanently managed from the Directory Sync (DirSync), and if DirSync was disabled or removed, the user account became stale. The only thing that you could do to manage that user online was to reset their password. You could not delete the account, and couldn't modify other aspects of the user account.
The addition of this alleviates many headaches for those out there moving from BPOS (used DirSync as a migration tool) to eliminate the on premise server required to run it. Moving to Office 365, former BPOS customers can now manage their users online without that need. This applies to many small businesses that were frustrated with the need to continue to have another server that isn't a domain controller, on premise to run Cloud based mailboxes.
In addition to this, I recently ran into a similar scenario where I was extracting mailboxes from a an envioronment over the 1,000 limit to use the batch migration. Since these mailboxes were being extracted for the purpose of an acquisition, the installation requirement of Directory Synchronization in the staged migration scenario (note that you can run a staged migration on 100 users or less without Directory Sync). I then was required to run Directory Synchronization, at the risk that the mailboxes I was extracting would become stale longer term, and if not setup in the acquiring companies Directory, could eventually be removed by accident or deteled. Note that I had to run a filter of MIIS to ensure that only users with a specific attribute in the Directory could be copied to the cloud.
By disabling Directory Synchrnization I can then modify those accounts, and evenutally make them Cloud only. And longer term, enable a new Directory Synchronization to take place with no risk.