The stupidity of that in One Moment in Time is amazing.
Actual footage of Quesada narrating it at Marvel:
Anyway, here's the simple thing. The continuity happened one way until OMD, and per the deal Mephisto said a "small part will remember" and then he changed time, and OMIT simply showed how things are remembered in the new continuity.
So all you need is Peter and MJ to get the original versions and they can remember their marriage, the original deal and then the altered timeline memories on top of that. Then going forward you can simply ignore or skate over "One Moment in Time" forever.