That's a good idea, recreating your users properly synced from AD.
The phone directory comes from the "Telephone Directory" form on the controller. You can import stuff into this form using a .csv file, but I don't know about populating it via an LDAP lookup. Smarter/special phones can do LDAP lookups to populate their directory, but not normal phones I don't think.
But I have to ask, if people have access to the MiCollab directory via their desktop client, why would they even look at the clunky phone directory? It's not very usable, and it doesn't have your Outlook contacts in it like the MiCollab Client does.