Yeah, it's a terrible scene. But it is important to the movie.
I saw an interview segment with the writer (maybe on the special features) where he explained the symbolism of the scene and why he wanted it to be so cruel. Supposedly, it's meant to symbolize how the country was abandoned and left to be *raped* by the Taliban and others.
The fact that it involves children who couldn't fully understand it at that time is what is really hard to accept.