I really hate the OMD story and the way it diminishes Peter in my eyes, this is the flagship character of the Marvel Universe who is making deals with the devil. If this was someone like the Punisher it would've been more acceptable. And regardless, I see it as a cheap cop out, a deus ex machina. It would've been easier to have them stay divorced. But I think Marvel realized they put themselves into a corner with the whole secret identity exposed storyline.
Despite my anger I got around to reading the post BND stories and found them to be getting better and better. It really picks up with the introduction of Jameson's father, builds steam with the Mayoral election (and the eventual winner was a big WTF moment for me and really shook up the Spidey cast in many ways). American Son was great stuff and with the exception of the Black Cat story, the recent stuff is fun as well.
It's been hinted that Peter and MJ are aware that their timeline has been changed. And if you notice the two of them haven't been shown talking directly to cue the readers in. Part of me knows that eventually this whole thing will be ret-conned and/or forgotten just as with many storylines. For instance it's been forgotten that Flash Thompson was in the Viet Nam War and now it's shown that he served in Afghanistan, John Byrne's rebooting of Spidey has been ignored, and so on. Just as I knew that Steve Rogers would come back, I know that this will be history but it probably won't happen until Quesada is no longer in charge.
So for now I have a screw it attitude and try to be patient.