I may be wrong, but didn't residents first come to Onbu through contamination? As if these beings did not exist before/no one knew about them? And then there are also several that start roaming around?
I find the ending you suggest somehow comforting, but also bleak. And the idea with the clues I really think is quite brilliant.
Why not make the ending one of simply finding a place where Onbu can hopefully rest forever. It lies down, stops listening to the player and starts to rest, in between it still draws attention to itself, in the beginning by occasional noises and movements. Nothing threatening, like when dogs dream something nice. But it becomes quieter and quieter, sinks into a kind of hibernation. And instead of dying and decaying, it becomes (again) a part of the landscape. And in the end, the only thing left to remember Onbu by is a small hill with a village on it.
