Just so you know, the creepy Trading Sequence girl is named Fado.
You brougt up some great points, but I feel that the Kokiri just don't share our view on the world. They don't really understand death, so the "punk kid"'s fate would be humorous to Fado. I don't really feel that the Koiri's minds work quite like ours, with a view of what is evil and what is good. I think that they do not have memories that function like a human's or Hylian's. That's why everyone believed that Link was a Kokiri--they don't truly "remember" when he was a baby, and since they never were, they cnnot connect to him. Even Navi was different from the Kokiri's silent guardians, for having a will of her own and no Kokiri to watch over. They were unfamiliar with danger, but I think they also had an extrasensory ability. They know that Kokiris cannot survive beond the woods, where the Deku Tree's blessigns of eternal life do not apply to them. But they also cannot die like humans or Hylians- they simply fade when they go beyond the Deku Tree's power. Mido teases Link, and I may be mistaken, but he's one of the only few Kokiri left later on. This is because the veil of innocence that hid Link's true idenitiy from them was not affecting Mido, whcih is why he always teased Link about not having a fairy. Saria, being who she is, also knew that you were diferent, because she also was...well, more mature than the others. Fado and the creepy humping guy, however, had this curtain from the real world. Without the Great Deku Tree, they faded, but Mido and Saria didn't because they understood. The humping guy, having no need of reproductional organs, did not understand what his movements suggest.
I hope I got all the typoes(I make a LOT of them) and that my little theorizing thing helped you understand the Kokiri. They aren't really easy to...comprehend, and I could be wrong, but this is how I think all of this happened, and why.