Look, I bet in the next year or two this whole thing is undone and Spiderman is back to the post clone saga status quo. There's already a few Deus Ex ways of doing it that they put in there:
-The 'part of the soul' that remembers everything (or does that 'part of the soul' only remember the marriage and not the other random changes they just decided to make)
-Whatever Mary Jane whispered into Mephisto's ear.
-The fact that they are some 'holy love' that only comes around every millennium or some shit like that.
-God
-Wolverine
-It's Magic
I betcha Marvel has some Crisis type event lined up to fix up the timeline.
My likely bet of what's going to fix it. He's like Deus Ex Machina with claws.
Or do you mean Deus Ex Wolverina?