If this Rikudou guy really did introduce ninjutsu to the world then it's likely he was the first to muck around with the dimensions in addition to everything else. That's not to say he created the technique, but something like bringing the dead back to life seems like something people would try to research very soon after being given a new and powerful tool like ninjutsu. Before most things gain a military use they have generally been known to scientists for a while. I think it's quite possible the first ninja we're more scientists than warriors but as the power and scope of ninjutsu was made more and more available it's military applications became more and more obvious and a war was started, leading to the formation of the villiages and organized ninja training etc.