I said before that Nidhogg, if he want to, he would stop the this vengeance against Ishgardians, but he will never do such a thing. Nidhogg knows very well that Thordan is dead, he like all dragons knows how mucch a human can live, they know too that something that could happen yesterday, for orther it would be centuries. He also knows that everyone living on Ishgard are Thordan's decendats, he was to punish his decendants forever.
Nidhogg doesnt wanted them dead, he doesnt care what happens, he was to punish them, to make them suffer forever. If he wants them all death, he have destroyed Ishgard long time ago.
Do you think that Ishgardians could have done something peacefull? let you remind what are the heretics and that Ishgard is under the rule of a corrupted Churt that knew the truth for the start. Ishgard's people was hurted so much with Nidhogg 's rage plus combine that to the wrong leading of the church to the point that they went fanatical zealots with their relegion. Everyone tring to do something suspicions could be consider a heretic, speaking with a dragon was a death penalty, lol they even dont trust anyone who was an outsider. Much of them were so fanatic that they even killed Au'Ra inocents, they were mercyfull only to recieve a worst punish. Another example is Estenien, his family was burn in one of Nidhogg's atacks.
Was not until a the arrive of the WoL, yes. But at that point, the actual rule of Ishgard has already started to be put into question, there was much hate bewetten lowborns and highborns. It was knew that the church could be corrupted.