I don't think the Ninja system is responsible for hatred etc. it was said in the Manga, before Rikudo came along, the world was basically nothing but war, he offered a new ideology and teaching, not only saving the world at the time from Jyuubi, but also seemingly stopping the battles that were everywhere, it doesn't matter what you do because every new version of peace gets twisted back into war, I don't think there is any true way to stop it.
If you think about it, right now the Shinobi alliance is essentially the Ninja world working as one, the only thing stopping peace now is Tobi and/or Madara trying to achieve peace their own way.
The Ninja Village system is essentially Hashirama's version of what Rikudo did, instead of teaching Ninjutsu, he taught them an organization system to better themselves, aside from certain villages being difficult, it was essentially a more peaceful world than it was in Madara's time.
Last edited by Xiraiya; October 20, 2012 at 11:15 AM.