I can get why you can't kill children in Skyrim. As far as I've gotten, you can't be KOTOR-dark-side-evil, at least not in the story sense. I know I killed a few innocents with no names, but that's about it.
However I absolutely can't get why you couldn't in "Fallout 3". You could be a slave trader in "Fallout 2". Heck, you could annihilate an entire town with a nuclear device in "Fallout 3", but killing children is where the devs draw the line? And yes, that town had children by the way.
That reminded me of an incident I had whilst playing "Fallout 2" back in the days when it was still new. I was never a child killer by choice, however one of my stray bullets, well strayed and ended a life of a six-year old. A total accident, as I was trying to shoot a guy 90 degrees to the side of that kid, with the kid being about a hundred feet away.
That child's prostitute a mother then started screaming and charging at me, her death was entirely my choice. The death of that child at my hands was one of the most powerful experiences I had whilst playing a game. It truly brought out the dread of that barren world. A world of cruelty, inhumanity and "moral bankruptcy", where nobody's clean, not even the protagonist.
I think that there is another reason why child murder shouldn't be exempted from games. It reminds us that murder is a monstrous act. Interplay interpreted it well in their Fallout-series: once you'd become a child murderer or a slave trader there would be some very dear consequences. In the first case a bunch of mercs would once and again appear on the world map to claim their reward for claiming a head of a child murderer and these guys were tough and well equipped. In the second case, if you would choose to become a slave trader that would forever screw your relationships with the democratic NCR, since you had a slaver tatoo on your forehead, "Inglorious Basterds" style.
In short, you could permit child murder, but don't make it consequence free. Children make great collateral damage. For what I see it, a murder is a murder, it is also a thing that games make you do 90% of the time. Killing a child with consequences once in a while could remind you that genocide isn't all it's cracked up to be... and killing a child from the shadows with no witnesses (or perhaps disposing of witnesses) would teach you that some people get away with it, you know, if you want realism and shit.