Yeah, if you bother to read (or re-read) the 35-50 quests prior to "Fray" being exposed, s/he basically hijacks it and writes sardonic text instead of the usual objective and compassionate entries. The ending one (before the battle at Whitebrim) even says something like "You've been called to Whitebrim, where you may be forced to surrender your weapon. Well, nothing to do but go there and kill them all." And yes, "Fray's" gender is changed depending on your character's sex as a means to foreshadow the truth at 50.
Regardless, the point of being a DRK is that you're someone who has seen the ugly truth - that without your mask of heroism, you're just a thug who kills stuff for a sporting battle, and deep down you might hate people for forcing their problems on you and being ungrateful when you pull through for them. To give into those dark impulses would make you nothing more than a common criminal, though. What makes you a Dark Knight is that you've seen and accepted that ugliness - and fight on anyway with no illusions that you're good or righteous. Dark Knights fight not out of duty, religion, or custom, but purely because they choose to. They make sacrifices of their own righteousness to do what must be done under no delusion they're heroic at all.
In that sense, they're the perfect Job for the morally grey Dragonsong War.
I did not agree to kill Nidhogg because I wanted to or believe there would be glory in doing so, but the modern smallfolk of Ishgard are in no way responsible for Thordan and his Knights' sins and deserve to be free of Nidhogg's endless torment. Diplomacy being impossible, my hand was forced...
This does not absolve the Holy See of hiding the truth and perpetuating the war under false pretenses. If they refuse to show their ugly side to the world, I'll drag it out of the darkness with my own two hands.