Maybe that's just what the Thordan line wants you to think :P Maybe spin it from a tale of rebels causing troubles between the dragons and Ishgardians into a righteous story where Haldrath avenged his father and began Ishgard in his honor.
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I think its just as likely Nidhogg is corrupt. All we have seen strongly points to him being a enemy dragon. He is certainly been portrayed as very hostile and full of hate, particularly with the impression we get from the Dragoon quests. Hell, he even looks like a nasty black spiky dragon as opposed to his apparently more benevolent falcor looking brother. Rage, hate and darkness seem to be his thing.
It's pretty clear Nidhogg is corrupt and we'll probably have to put him down by the end of Heavensward, but we don't know what drove him to such a state of madness. Popular theory and the in-game explanation is it's because Haldrath gouged his eye out and took it as a trophy, but that's just Ishgard's side of the story. If there's anything Ysayle's right about, it's that we (and all of Ishgard) are unthinkingly fighting a war we don't know the purpose of.
Besides which, history is written by the winners. So while nothing in-game hints that my whole "Shiva hypothesis" is true, it's also possible it is true and all of that was covered up by the Holy See to solidify their grasp on power. A curious thing is that Ishgard's founder is "King Thordan I," while it's current ruler is "Archbishop Thordan VII." Hmm...
Likely when the first king died from dragon-mind-powers and his son took to war against him. Halone led the people there, and likely the people turned to a more religious doctrine with the loss of their king. Haldrath probably became the first Archbishop, leaving the other four houses to be the royal houses for the new city.