Watched the finale at Betty's place, she was a sobbing mess by the end. Unfortunately I was too distracted by the technical details to really feel John's pain.
So let's see, no one witnessed the entire incident. John only saw about 2/3 of the fall, thanks to Sherlock's clever dictation about where he stood at the start. As soon as Sherlock leaps off the edge, John naturally started walking towards the scene, which meant he missed the final 1/3, and just assumed Sherlock jumping off = the body on the ground.
The passers-by only saw/heard a body hitting the ground, it could have come from anywhere, for example, from the window on the 3rd floor. And that's where Molly came in. She could have easily got hold of a random body of roughly the same built as Sherlock, dressed it up.
As for the shot of dead Sherlock's face. Well, it's human instinct to shy away from such horror, nobody really pays that much attention to a corpse's features.
So my guess is, Sherlock jumped off the building, grabbed onto something half way through the fall, which was when Molly chucked the double's body out of the window. While all the chaos unfolded down below, Sherlock had plenty of time to pull himself up and get away.
Now, I shall be disappointed if John doesn't bitch-slap Sherlock at the start of season 3.