Except we didn't--it was just Anderson's theory, played out large for all to see. The process was repeated twice, once in a ridiculous slash scene and again with Sherlock's (misleading?) explanation. Anderson's theory explained the fate of Moriarty's body, but Sherlock's seemed more rational. But I wouldn't put money on either of them--I know Moffat's trolling ways far too well.
Either way, Sherlock and John's reunion was everything I wanted--particularly the three punches. Sherlock may be a genius, but the average Whoniverse alien has a better understanding of human emotions and psychology than he does. Nothing John said would convey his frustration and anger--so bring on the punches.
The actual plot of the episode was wonderfully, brilliantly British. While some Americans may miss the historical significance of the 5th of November, the episode had enough references for uninformed viewers to get the gist of it. It also alludes to Alan Moore's graphic novel V for Vendetta. And that was just one of the in-jokes and allusions in the episode. The motorcycle and helmets that Sherlock and Mary used to rescue John are probably the ones used in "The Bells of St. John." And if Sherlock's explanation is correct, he was listening to John's grief, just as Eleven was in "The Impossible Astronaut." Even the episode title not only alludes to the original Doyle adventure, but subtly foreshadows the railway carriage.
Finally, the casting of Sherlock's parents and Mary is hilarious, especially in light of this old interview:
Interviewer: Are you going to be able to keep your actors after season 3? They’re both quite big stars in The Hobbit..Moffat: Yes, but we have their families locked in the cellar.I guess he decided to let them out for filming (Sherlock's parents are Benedict's actual parents, and Mary is Martin Freeman's partner.).