I don't believe the reasoning was ever clearly revealed (Never read Hyrule Historia, so I don't know about that), but I always thought it was just because the Kokiri don't really die if they leave the forest. It could very well be a lie told by the Great Deku Tree just to keep the Kokiri from ever getting curious about the outside world, and exposing them to the danger in it. It makes sense, because what could a Kokiri actually do to defend themselves outside of the Kokiri Forest? They're functionally little children, and would probably be killed very easily since all of them lack any real combat experience, so that's how their guardian defends them; telling them that they would die if they leave the forest.
...Actually, that could be what the Great Deku Tree meant the entire time. Kind of a half-truth maybe.