If you could kill off one of the scions...

[Cilia]

Snip

Not going to get into the Ul'dah debacle, cuz that's ancient history and I don't care for how it was resolved anyway.

While we are down to two combatants and a secretary (one combatant of whom is prestigious but not exceptionally gifted), it's still the Scions' MO to kill primals. That is the one thing people can always count on us to do, no matter the situation - rain, shine, sleet, or snow, we will quash any primal that shows up because of how dangerous they are. Preventing summoning is a more favorable option, but we can't always succeed at that. Even with only Alphinaud and Tataru (and later Y'shtola as well as Cid, who may as well be an honorary Scion at this point), we still fulfilled our mission.

On Nidhogg, yes, he does not see Ishgard for the people within it but only as an entity that has wronged him, and thus he carries out his eternal vengeance. It is this entire viewpoint that is fundamentally flawed - 99.9% of modern Ishgardians are lied to in regards to why they're in an eternal war with the Horde. Even if they are ignorant as to why they're fighting the war, you can't really blame them when the only options are to fight and kill or death by dragons (or the third option, become a heretic and probably a dragon yourself). If the Ishgardians don't know the real reason behind the war, how can they possibly learn from Thordan's sin?! This is the real reason Midgardsormr states he is going to "join in the chorus" - he wants Ishgard to learn and grow beyond Thordan's mistakes, and offers them the chance to do so now that they are armed with the truth.

Nidhogg? Nope, he just wants them to suffer more. Forever. What he is attacking is not individuals, but Ishgard as a nation - it's the concept of the country that offends him, not any individuals or particular aspects of it. Nidhogg has no interest in peace, or getting Ishgard to learn from Thordan's mistakes, or anything beyond his vengeance. No matter how many lives, mortal and dragon alike, are consumed, he will never stop. While this is understandable, it's not quite relatable, and in no way is it justifiable. He does not want to win the war - he just wants Ishgard to suffer. Forever. Let me stress that: FOREVER. Estinien acknowledges that Nidhogg could have won the war pretty much any time he wanted to, but he has no interest in winning so that more Ishgardians might suffer his wrath. It's a war on Ishgard's spirit, the very concept of Ishgard, not any one person or anything that makes up the whole.

Putting aside the fact Nidhogg never trusted the Ishgardians in the first place, it's not quite the same as seeing your sister's murderer thrown in jail for the rest of their life. It's like exsanguinating said murderer to the point of unconsciousness, then giving them a blood transfusion so you can do it again for as long as you like. Then doing it to said murderer's spouse and children. Then their children, and so forth. It's sadism of the highest caliber, and there is no "justice" in that.

Why should the dragons put their faith in men and believe there is good in them after Thordan's betrayal? What proof do they have it won't happen again? There is none - that's why it's called faith. Even without proof, you simply believe.