Yeah that's the thing with all the "Moriarty is alive" theories. It asserts that Sherlock Freaking Holmes can't tell a gunshot wound to the head when it's literally right in front of him. No, I really hope he's dead. I just think they shouldn't have had a shot of Moriarty with the gun in hand. I feel like a lot of times this happens in shows and films because it makes for a nice tableau... but it's just that it doesn't fit, and that is also something Sherlock Holmes would notice. So Moffat should have.