The linked article does not present an accurate sketch of the movie.

(1) The sniper, in the story, saw the grenade before firing. He doesn’t kill first and later get vindicated.
(2) Both were shot while trying to throw the grenade. It was thrown, but didn’t quite reach the target.
(3) Some of the characters in the story play the part of innocent Iraqis. Some are shown as aiding the Americans in their fight with insurgents. (Who, by the way, are now, many of them, with ISIS.)
(4) The sniper is shown sparing another child who attempted to line up an RPG on Americans. The sniper waits to the last possible moment, and the kid loses his nerve when he’s not strong enough to hold the form-him-too-heavy weapons steady. In the movie, the sniper is greatly relieved that he hasn’t had to shoot.
(5) In the whole movie, no Iraqi civilian is portrayed as having been shot by the sniper. Only combatants. Unless you want to call “civilian” a person who is an active combatant, carrying arms and firing on Americans, just because he or she is not in uniform.

In January, Warner Brothers released American Sniper, an Iraq War film that portrays Iraqis as an undifferentiated mass of terrorists and terrorist sympathizers who can only be confronted with violence. In one scene, the film’s protagonist and namesake shoots an Iraqi woman and child to death — an act the film tacitly approves by later showing them as having carried a grenade. The morality of killing Iraqi civilians is raised only so that the hero protagonist can shout down whoever has had the gall to question his decisions by explaining that those civilians were no innocents.

Now whether the movie was an accurate depiction of what happened is another story. But the article is talking about what the movie showed.