Civilians Killed in Afghanistan

I'm not sure if this article caught my eye because I feel I know little of what is actually going on in the war or if I was curious to see how the Times would spin this story, providing their own interpretation as all journalists do.
The angle was clear: yes civilians were killed in the shooting, but in the split second the soldiers have to make a decision if a vehicle coming at them is in fact dangerous, the soldiers have a duty to protect themselves.
I'm not exactly sure what side I feel more comfortable with and that's mainly because I feel that such instances are not so cut and dry, that there are a lot of factors that play into every one's actions and decisions made.
What really concerns me, however, is that no system has been developed between the Afghan government and the American forces that would allow for adequate checks at these check-points and along highways as well as a different system of symbols as clearly the one in place is not working. Along with that, American forces perhaps can aim their fire at stopping the vehicle rather than the people inside. Afghan officials suggested the tires. All of these things combined could perhaps allow the citizens to feel safe traveling the roads and the soldiers safe to patrol.
Unfortunately, a reality of war is that civilians will be caught in the cross fire from time to time. However, I feel it is the American forces duty to make sure this is not a frequent occurrence, especially since these civilians have suffered enough at the hands of the Taliban.