T.o.b.y.,
Although I enjoyed 'The Empty Hearse', I too found the story of the snipers a bit strange. If Mycroft's people were capable of 'persuading' John's sniper to call off his attack after Moriarty's suicide, there was no need for Sherlock to fake his death. I did consider that Moriarty may have positioned others around Bart's to witness Sherlock's death (after all there were around 10 sniper sights trained on Sherlock and John at the end of The Great Game!), but if that was the case they would have surely seen the elaborate preparations being carried out to break Sherlock's fall. So Mycroft's people could have apprehended the lone sniper at any time during the Sherlock/Moriarty confrontation, Sherlock could still have taken out Moriarty's network, and John would not have suffered 2 years of emotional torture.
Having said that, it would have been much less entertaining than two years of Reichenbach Fall conjecture!