Dirsync is running fine now, so I would hesitate to suggest a reinstall.
The problems mentioned go way back, where the first Dirsync installation crashed and never got back online. After a long period without synchronization they decided to ditch the old dirsync and do a fresh install.
My guess is that the ghosted users were deleted onsite during the months without an active dirsync, and the deletions never made their way to Azure.
