Since we only can post our theories about "what might have happened", this definetely should go into the theory section.
Besides, I really don't think that Nagato killed Yahiko, more likely Yahiko got killed during the war, and Nagato reacted this way, wanting just peace...in his weird way. I can very well imagine that other characters in Naruto would have reacted the same way, when their most important people died - just look at the current Naruto, and it was "only" Hinata who "died" infront of him, imagine Pain would have stabbed Sasuke or Sakura <_<
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