Know it's an old thread, but was looking for the same.
We do not have all AD users with dual emails, so it's not the biggest pain...
Thanks to FrankSc, found what I was looking for.
When a ticket is created with a non discovered AD user, it will create a Helpdesk user, and "You can merge an existing Helpdesk user with an AD user. There is a "Merge with Active Directroy or Workgroup user"-button next to each user, far right."
Hope it will help the next person, who is searching and finding this thread.