There was never a sniper watching Sherlock. The sniper's target was Watson. The targeting scope was squarely focused on Watson, so when he got the "go" order, he'd pull the trigger and instantly be done.
The sniper didn't hold off shooting because he saw that Sherlock was dead, he held off shooting because he received a message to not shoot. Just as all the other assassins in other parts of town were focused on their targets, not personally observing Holmes, and were getting their orders via phone messages, the same is true for the sniper.
Since the entire rest of the world, except for those involved in the ruse, all thought Sherlock was dead, whomever/whatever was monitoring was not in a position to see the charade.
Furthermore, though I'll have to recheck, but in order for the sniper to be concealed and in a position to shoot Watson, he'd probably have to be in the same building or same side of the street as Holmes, and not in a position to see, without sticking his head out of the window and giving away his location.