... and why would she team up with Michael? I doubt without Harry she would have even known Micheal ...
You forget: Michael has some extra guidance!

Without Harry's assistance, SI & Murphy will have needed some extra help... help that Michael is well-situated to provide! Obviously, that's no guarantee Jim will have written it that way; but it'd be a nice exemplar of God's Providence, with Michael's multiversal presence situated to support Murphy (or in a different Alt!Universe, Morty?) when that alt!Harry does not.
... For the record? If you really want to torture Harry, have Murphy act like he never existed, and treat him that way as well with a totally closed mind towards the supernatural...
Murphy 1st met Harry in the Restoration of Faith short, earlier even than Storm Front.
He was a regular consultant for SI, for the first few novels (the earliest such (that we see onscreen) he had already been consulting with them for a while).
All of that is the same, between the "prime" and "Mirror" universes.
The entirety of the setting & character-development isn't subject to revision -- only from GP's "choice" onwards.
I don't see any way for Mirror!Murphy to have buried her head in the sand and deny the supernatural; and Harry will *very* much be on Mirror!Murphy's radar -- as a Bad Guy
(tm)!