My guess and speculation. The Nue would be appeased not killed because why would there be subplot of Yamato's ancestors being Umi Nue worshippers. Unless of course the monster Nue is different from the myth Umi Nue.
It is possible , if Nue is connected to Yamato family then her close death trigger it to surface, Also possible that Illuminati wannabe is involved,
If they appeased Nue then Myst might conspire to get a hold of the siblings cause in their minds Japan managed to control Nue.
....... If the appeasement involve human sacrifice we riot,