For context, as another anon in this thread has stated. JMS' original pitch for OMD was that he didn't just want to undo the MJ wedding, he wanted to undo pretty much everything past 1971>When I was halfway through issue three of OMD, we received Joe's script for issue 4. After reading it, we (Axel, Tom and myself) all quickly realized that we had a problem -- the script we had just received was not the one we were expecting, and the events that were being set forth in that issue were going to conflict with the work that was already being done on "Brand New Day." I thought that perhaps Joe had forgotten some of the stuff discussed at the summit meetings and the subsequent e-mails and discussions that followed, but that didn't seem to be the case; this was the story he wanted to tell. In his story, Mephisto was going to change continuity from as far back as issues #96-98 from 1971. In Joe's story, Peter drops the dime on Harry, and that helps get him into rehab right away. Consequently, MJ stays with Harry, and Gwen never dies and never has her affair with Norman, etc., etc. And in the end, Peter and MJ are never married.
Editorial said no to this, partly because it would mess up their plans for BND, and partly because it would have a catastrophic effect on the past 30+ years of Spider-Man canon, so JMS went along with Quesada's plan for it instead (With JMS wanting to have his name removed from the later issues because he took issue with Quesada's "It's magic, we don't have to explain it" excuse for Mephisto's deal).
JMS tried to use this opportunity to retcon Sin's Past away, which he assumed he'd be allowed to do, but editorial told him no.