In the revised timeline, a random mishap during Peter's activities as Spider-Man caused him to be knocked unconscious when he was due to attend the wedding. Rather than reschedule the ceremony, they chose to cohabitate as an unmarried couple during the period in which they were previously married.
Mary Jane's pregnancy did not occur in the revised timeline...
... according to Spider-Man's entry in the Official Handbook of the Marvel Universe A-Z #11.
The relevant passage of text states that:
Despite money from a sympathetic Tony Stark, and tapping every paranormal and superhuman resource, Peter could not find any way to save May until the demon lord Mephisto offered Peter and Mary Jane a choice. Mephisto would restore Aunt May if the couple sacrificed their marriage, erasing it from history and losing all memory of it ever having occurred. Knowing Peter would never forgive himself for allowing Aunt May to die so that he could remain happily married, Mary Jane agreed, followed by Peter.
Thus, the couple's marriage was pulled from the timeline and Mary Jane never became pregnant, though all other events in Spider-Man's life still happened.
It was later explained in Amazing Spider-Man Vol 1 #639 that since Peter's activities as Spider-Man were the reason he failed to show up to the wedding, MJ decided she wouldn't marry him, or have children with him, as long as he continued to be Spider-Man. She didn't want to leave him either though, so they agreed to continue their existing relationship as an unmarried couple, until and unless there came a time when Peter was willing to give up his costumed identity.