Forgetting the "how" of how things went down, the "why" also came from left field as well. The darkness and cruelty of the human race were, at best, a weak motif in the arc anyway. Are people bad, sure. Are groups of people bad, sure. Humanity having a bent towards darkness? Not so much. The kind of Kojima, MGS cut away to real world atrocities was completely outside of the story telling styles established to that point.
Even ignoring how the theme came about. Where else is it used or explored in the arc (or other arcs for that matter)? It really felt like a quick hit that was used to give some complexity to the human race so the lines in the man vs monster battle would be blurred a little.