Hi Yordan,
Here is the detailed steps about the step two.
1. Deactivate disrync service . Go to portal.microsoftonline.com/.../ActiveUsers.aspx and click on “activate”
2. Remove the synced user “John” and “Smith”
3. Install Office365 Powershell and connect to Office365 service technet.microsoft.com/.../jj151815.aspx
4. RUN “Get-MsolUser -ReturnDeletedUsers | Remove-MsolUser -RemoveFromRecycleBin -Force” to remove all the users from Deleted user Queue.
5. Change the local user’s SMTP address and make the address unique.
6. Re-enable the disrync service.
For your question : The users still can log in to Office365 service via the ADFS server after the dirsync service is disabled. However, We still recommend you can do that in a non-peak time. (like : off-work or weekend.)
Best Regards,
Neo Zhu