He knew the worms were down there and what they were capable of so why in travelers sake would he allow them to continue into the deep after they ignored his warnings. The sisters had no power then and he could have easily stopped them from unleashing the evil of the worms. Instead the sisters go on to become gods and the Leviathan gets eaten.
Been studing the lore alot more as of recently and this kinda bugs me. Maybe i missed something
-
My opinion? I think it's something having to do with the nature of the Light. The Leviathan is described as the greatest disciple of the Traveler and an old priest in the fragments. I believe that there's some component of the Light that compels him to allow them to make their own choices. There's no in-game explanation, but this is my best guess.