The new Outlook Add-on has additional features over the old Integration so you might want to check to see if that helps at all. When the User is uploading the Email into the Repository, the only live check is if the File name already exist in that same folder which would provide a prompt on what to do in that case.

If you are using a Default Email Template, and you capture the Unique Message ID and Conversation ID as Metadata in your presets, then you could craft a WF to check if those ID's Match an Email already in the Repository.

The Conversation ID never changes for that email, where the Unique Message ID is changed for each Reply/forward etc. If you are going to use Versioning with the Email's, make sure your Unique ID is a multivalue field so your search would find any other of the versions of the email for matching purposes