Aw, anon, it’s okay. I don’t think it’s going to go down that way. Among other things, have faith in the BBC’s joy at getting all this great worldwide public attention!
But also have faith in the fact that even in the episode where John and Mary got married, we didn’t see their vows. We saw Sherlock’s. We saw John struggle harder to decide whether to take back his pregnant! wife! than he did after Sherlock went off for two years and left John to fall apart in grief just to satisfy his own sense of drama.
We saw that after one month with just Mary, John was starting to lose it. He needs Sherlock, even if he has a family.
And to be brutally honest, I’m not seeing how that baby’s got much of a future. I am fairly confident that season 4 is going to get pretty darn ugly in some very personal ways for Sherlock and John (and if it doesn’t, then season 5 is likely to be worse), but I don’t think you need to worry about them ever abandoning each other.
(Also I really highly doubt that that is actually Moriarty. It may be some scheme he arranged to go off in the event of his death, but I think Moriarty’s dead. Remember how, at the beginning of the season, Mycroft asked if Sherlock was really sure he’d finished off the last of Moriarty’s network?)