In practical terms the final two issues were written by Quesada himself so no the execution wasn't "all his".
JMS had every single practical idea for doing the story well, shot down.
-- He wanted Aunt May getting shot to lead immediately to OMD, instead Quesada and others asked him to pad it out with stories*. That killed the dramatic tension, the desperation, that could justify Peter potentially making that deal. If Aunt May was shot badly and was seconds from dying and Mephisto came in and stopped time and so on...then you could sort of justify that Peter could do it. It's also right after May got shot before his eyes, so emotionally it's like Bruce-in-crime-alley-seconds-after-Joe Chill, so you could make it work on an emotional level. But if you drag it out, with many issues with Aunt May in the hospital on her deathbed, with Peter going out and doing an awesomely badass beatdown on Kingpin, with MJ and Peter canoodling atop ESB, and "The One Above All" telling Peter it's gonna be okay, and also fighting Jonah in a boxing ring...that's not gonna work. The story now read like a dude for days processing his Aunt on deathbed simply not accepting reality. That's how it came across emotionally.
-- JMS also wanted Peter himself to make that deal, and not MJ, feeling that it would come off as cowardly to a lot of people that Peter is passing the buck on to his wife to make a deal that would bail him out. These two were among the major complaints for that story among readers. JMS wanted to provide a detailed explanation for what the timeline changes did and did not do. Some of that included stuff like Gwen being alive which Quesada let him believe for a long time he could have done.**
So I don't see how it's possible to hold JMS responsible for this.
He never agreed with the story and only did it as a favor to Quesada, and out of friendship and loyalty (and surprising as this is, Quesada and JMS are friends...JMS wrote Thor after finishing OMD and the public fallout about that after all and continued working there until about 2010), so he was willing to affix his name to a very controversial story, and then had all his suggestions and ideas turned down. So to me, JMS was the guy who was a real mensch about this, and Quesada mismanaged his side of the story. JMS' mistake was removing his name or threatening to after the first two issues came out. What he should have done was refused to do the story flatout and tell Quesada that he wanted to finish his run on his terms, and then another writer or so on can do the story that Quesada wanted or Quesada would write on his own.
*The irony is that these "Stopgap" stories ultimately provided masterpieces like Back in Black and "To Have and to Hold". It's not a good look that the only great stories directly made possible by OMD aren't the stories that came after, but the ones set directly before written in part to prolong and extend the status-quo that OMD claimed was bad and so on. Fraction's annual was a pre-emptive protest against OMD.
** And as for changing the timeline to bring Gwen Stacy back. Many fans here might object to that for changing too much, and many creators did at that time. But let me say that if they had done that, if they undid the marriage and continuity and brought back the Lee-Romita College Era and made that the default status-quo...that actually might have worked. Because the Lee-Romita era is charismatic whereas BND is not charismatic at all (it's the least charismatic period ever). If you bring Gwen back, you are trading one failure for another. Peter got something out of that deal, as opposed to OMD where he got nothing back (and no Aunt May and Harry Osborn, emotionally, aren't tradeoffs). Having Gwen back, would mean that when Peter and MJ date later on, it would be without the issues and baggage of Gwen's death between them, and that would be a totally new thing in 616 for those characters.
So while I agree with JMS and think that undoing the marriage was a mistake and unnecessary, if it had to be done JMS' concept seems to have been the only one that could have maybe made it work.