... For example, it's possible Alt-Murphy will draw a weapon and start shooting at Harry the moment she sees him, because Alt-Harry is one of the bad guys...
100% this.
We know that the decision causing the MM divergence happens "at the end of Grave Peril," but not what that decision is, or how close to the end of the novel.
But we know that Murphy got trapped by the Nightmare who Fake-Harry'ed its way in. A year later in SK, she's still combining drugs & alcohol to damp things enough to get a night's sleep (that was a huge trauma for her) and if Mirror!Harry isn't as supportive after SK, this could be the souring of their relationship... Harry turns to darker paths, makes deeper compromises; Murphy trusts him less and less; and by the time Harry!Prime gets to the Mirrorverse, Murphy sees him solidly as a BadGuy.
That said, not a shoot-on-sight target; but certainly an armed-and-dangerous / hand-on-holster / do-not-trust individual.
Imagine a worse case scenario for Harry. He is forced to kill Alt-Red Court Susan. She won't be the youngest vampire any longer. There won't be a noble cause behind Harry's actions, just Harry surviving a terrible situation. Something like that would change what Harry feels in big way.
One of the very-real possibilities of Harry's "decision" is that he decided to trade Susan to Bianca, when Bianca made that offer (at the beginning of the climactic fight). In that case, "Susan" is gone and only another blood-sucking monster exists in a Susan-shaped fleshmask.
Or, Bianca could have spent the intervening years using the Rampire's time-honored "Jaguar Warrior" training-methods to brainwash Susan into fanatic loyalty.
Either of those would be their own whole serving of trauma for Harry!