Creator Backlash: Probably one of the most famous ones in comics, from J. Michael Straczynski. Contrary to popular belief, JMS wasn't against the storyline. Instead, he was angered over the fact that Quesada didn't allow him to fully explain story, leading to the rather infamous "It's magic, we don't have to explain it" quote. Things reached the boiling point when JMS actually threatened not to put his name on the final issue. Following the completion of the story, JMS would completely disown any involvement, place the blame on Quesada, and commence work for DC Comics.
Running the Asylum: The story was based off of Quesada's desire to return Peter to his single lifestyle.
What Could Have Been: According to Quesada, JMS wrote the point where the new timeline diverged from the old one as be Harry getting into rehab back in the early 1970's, thereby affecting relationships and meaning Gwen Stacy never died. Marvel's writers collectively nixed it beforehand because such changes would affect the entire Marvel universe and invalidate nearly forty years of canon, and with two issues done they had to scramble to change the remaining two at the last minute. (If true, this could explain why JMS wanted his name off those issues; but all things considered, take this with a grain of salt unless we hear JMS's side of the story.)
Though if they had gone through with resurrecting Gwen it would have been some major Fridge Logic because had Gwen not died she and Peter would have been married by this time which defeats the point of wanting a single Peter.
Writer Revolt: There are a few subtle hints that the writers didn't want to go through with this.
Writing by the Seat of Your Pants: Covering his bases, JMS (Or Quesada, or probably both) snuck in some emergency "backdoors" in case Marvel balked on OMD after a while or decided to produce a sequel to make the BND continuity more "acceptable", and had MJ make a secondary deal with Mephisto to make a resolution somewhat necessary if sales and fan outrage demand it.
Ultimately averted (even though sales and fan outrage arguably did demand it); turns out MJ was just reaffirming the deal with Mephisto.