I forgot about that completely! And Cory had no reason to lie.
I think that he had plenty of reason to lie. But even if he was not lying, he is an unreliable source without corroborating evidence.
First, the reason to lie. Based on facial expression, line delivery, and common sense, Corypheus seems to have viewed the fact that the City was "black" and "tainted" to have been a Bad Thing. If that's so, then it would be perfectly understandable for him to have self-deluded about agency. If Corypheus and the other magisters had found a City that was already tainted, then its tainting would not have been their fault. He could, psychologically, avoid responsibility for that action and its consequences. People do this all the time, from relatively innocuous things (the refs jobbed us! the fuel indicator was faulty!) to actual crimes.
More importantly, though, Corypheus is a problematic source. Importantly, he appears to have autopsy of the Tevinter expedition into the Fade. Autopsy - personal experience - is an important thing for any source to have. It's difficult to relate details about events for which somebody was
not present. However, there is a whole raft of things that push the other way. Personal experience is necessarily constricted and skewed by perspective even when there is no active attempt to deceive. Memory is inexact, and the events in question took place literally Ages ago. (Corypheus' memory and perspective are particularly suspect because he appears to still consider himself a Tevinter magister rather than a darkspawn.) And finally, there is literally no corroboration for some of the things he says. As Sebastian points out (along with Codex sources etc.), Tevinter magisters had documented that the City
was, in fact, golden. They certainly
could all have been wrong somehow, but it would take more than a single extremely sketchy source to overturn Ages of historical orthodoxy.
There might be other ways to square the circle. Perhaps, say, Fen'Harel (or some other being) facilitated the expedition into the Fade and tainted the City itself shortly before the magisters got there, as a sort of vindictive or malevolent trap. But unfortunately, there is even
less evidence for any such explanation than there is for Corypheus'.