This is where it gets confusing.
The story says they never got marries but Marvel's Joe Q has said the marrige did happen.....but nobody remembers it any more.They remember events differently.
I think it's like the old question: "If a tree falls in the woods and nobody hears it, does it make a sound?"
If suddenly nobody remembers that Pete and MJ got married...are they married?
What I mean is this:
The events up to OMD happened. Then with Mephisto's deal he altered the memory of EVERYONE removing some memories and replacing them with new ones.
Instead of everyone remembering that Spider-Man unmasked and is Peter Parker, everyone's memory of the event doesn't include the knowledge that it was Pete underneath. Was that part of the memory taken out and not replaced, thus leaving everyone to wonder "Why don't we remember who was underneath?", or was it replaced with the memory of someone ELSE being underneath, or some other altered memory that doesn't leave people wondering why nobody remembers the results of something so huge in the media?
Peter Parker DID technically out himself as Spider-Man. But because nobody remembers that he did, the world doesn't know any better.
Same with the marriage. Everybody's memories of anything related to Peter marrying or being married to MJ have been altered to one that doesn't have him married. Perhaps people's memory now includes Peter missing his wedding, and Peter's memory has him "remember" it's because he got caught up in some big battle royale as Spidey and couldn't make it. And every other memory later-on referencing them being married has been replaced with one that references them dating.
So Pete and MJ DID technically get married. But because nobody remembers that they did, the world doesn't know any better.
And Harry? This is Mephisto's evil curveball...his twisting of the knife.
Harry actually did die in SSM #200. But when Mephisto went in replacing and altering people's memories of prior events, he saw the perfect opportunity to slip in extra pain to Peter: Mephisto resurrected Harry. And by simply altering people's memories of Harry's death and any later references to the event to one of him simply disappearing unexplainably, nobody will question why someone who's supposed to be dead is alive again.
Harry DID die. But because nobody remembers that he did, they don't question him being alive "again".
That's just the way I see it. If Mephisto simply went back and actually altered the actual events of the wedding day so that Pete and MJ never get married and let the following years just alter themselves you'd get a Butterfly Effect that would literally give us a DRASTICALLY different "Now" than what we actually have.
But if Mephisto kept the actual history of the 616 Universe intact and simply altered and replaced everyone's MEMORIES of those events, then there'd be no Butterfly Effect and no altering of where we actually ended up.
IMO, Mephisto altered and replaced everyone's memories of the past. The ONLY 2 actual CHANGES he made to the past were May getting shot and Harry dying, which is how they are alive and well now (since a simple alteration of memories wouldn't save either of them on their own).
And knowing this, you can STILL read the last 20 years of Spider-Man stories and know that they all DID happen just like that.