It makes it rather clear that Nidhogg never intended to win the war. But to punish all of Ishgard. The story makes it clear that all Ishgardians now posses the blood of Rastoksk, and that both heretics and loyalists are just pawns to perpetuate the suffering of Thoradan and his offspring.

Eistinien was willing to go along with the attempt at peace, but even Hrasveger, who loved an Elezen, was on Nidoggs side. As much as we might understand why Nidhogg did what he did, there wasn't much choice.

And as quests around Artryx Trine show, even dragons not part of Nidhogs brood are suffering because of the war.

On iPad, sorry for errors.

As an aside, Estienin wanted to carry the eyes beyond the reach of man or dragon, meaning he didn't have the means to destroy them.....

So, where Ratastoks eyes destroyed? How about Bahamuts?