It's simple really. Mephisto made the deal with MJ but Peter only thinks that his identity has been erased nothing else. The two of them have no idea that they were once married, that's the thing of OMIT. Mephisto must be having a good laugh over this.
Actually I don't think that's the case any longer.
In OMD, Mephisto makes a deal to save Aunt May with Peter and MJ in lieu of their marriage. It happened.
Mephisto then goes back in time and starts the domino that will lead to Peter not having married MJ. Then all that stuff in OMIT happens. And then when Aunt May is shot, Peter doesn't "repeat" his deal with Mephisto - that doesn't happen (As evidenced by Joe Q saying that he didn't see the red dove or whatever on his way back to the hospital to see Aunt May) - instead it's Doc Strange and Iron Man and Reed who solve Peter's identity issue in this new Mephisto-initiated timeline for Peter and MJ (with minimal ripple changes to the extended MU-616).
Actually, imo, MJ's plea-deal with Mephisto is a completely dud (from my viewpoint). MJ asks him not to mess with Peter any more. And Mephisto agrees. What MJ doesn't realize is that her timeline will be gone. And in the new timeline that Mephisto will initiate, the deal won't "re-happen" - so, Mephisto is free to mess around with Peter.
That's how *I* see it. JoeQ seems to say that MJ actually won and I just don't see how that can be. But that's probably cos this whole thing doesn't make "logical sense" - like JMS seems to have wanted it to do with his "Magic needs to have rules too" standpoint.
Btw, that particular viewpoint of JMS, I picked up from this
Newsarama article/interview with JMS.
Edit - And JoeQ still hasn't explained how the Disassembled storyline "didn't" happen. Or why Spidey went back to having webshooters.