That whole "Peter can't get involved with anyone else because MJ is still alive!" mess kind of shows a lot about Quesada's very bizarre pre-conceived notions, because a lot of the way Peter got back together with MJ and then, of course, BND, was all his editorial mandate.
We know that he: - Didn't want to get them divorced because he felt divorce ages the charcter (uh, having a contemporary friend who's been divorced five times doesn't?) - Didn't want to get them divorced because he feels that Spider-Man should be a role model (!!!!!) - Had them reconcile even though he didn't want them married because he thought that the marriage should be portrayed completely positively until it was undone.
Now, the last one was laudable in a sense because it was a nice change from the forced "we're too YOUNG TO BE MARRIED!!!!" of previous eras, but other than that, I think this shows that a really simplistic, black-and-white view of marriage and relationships; alternately put, it's a set of blinders that made Quesada look right past a really obvious place to naturally break up the marriage.
After Peter rescues MJ from her fake death, is a perfect time to execute a basic "couple cannot handle serious trauma and split" storyline, as adapted from real life. You would need a sensitive, talented writer to handle it (JMS?), but it wouldn't be difficult or complicated to plot. She's traumatized, and less able to handle the uncertainty his going out as Spider-Man -- also resentful of how long it took for him to find her. She feels guilty about how she feels. He can't figure out how to relate to what happened to her, and he can't spend as much time with her as she should because he has to go out as Spider-man. He feels guilty about all this, and about how long it took to find her. They both spend a lot of time trying to figure out who they are now as people and in this marriage, and eventually everything's resolved, but they realize that they're best friends, not lovers. Cue amicable divorce.
Give it a little time, and thanks to the Marvel sliding timescale, writers could subtly suggest (without outright stating and irritating continuity buffs) that this was a brief, meaningful but ill-advised marriage that stemmed from a rough period in both their lives. There are no deals with the devil, and since this takes place 5+ years ago, there's no remasking involved and thus no giant continuity snarls. Harry can walk back onstage at any point. Ta-dah!