Have they actually ever said straight out that new continuity = no pregnancy? After all, they've said multiple times that *everything* was the same except the marriage, which I would take as saying the pregnancy *did* occur.
Per Joephisto himself:
"The question sort of answers itself when you quoted my saying that "almost" everything happened. The funny thing about the pregnancy issue is that Marvel at the time scrambled to derail the story as quickly as possible. I don't know exactly how that story got as far as it did, but they ultimately realized it was a huge mistake. So, taking that into consideration, I personally feel that that's one that didn't happen, chiefly because Peter and MJ now not having been married, would have taken proper precaution to avoid getting in the family way in the first place."