I agree with the notion that Chaotic Grey Knights are not possible, at least not in any numbers that you could field them as an army. I'd say, if you like the Codex, or the challenge of converting Grey Knights to Chaos, go for a "counts as" army.
Further, I think making up a cool theme for an individual "counts as" army is much better and much more rewarding than making up some super-strange, far off explanation just to use the Codex. If I was fighting, say the fallen First Company, I'd say "Hey, cool idea!", but if I was fighting a horde of Zombie Grey Knights killed by a mysterious bomb that left their bodies and equipment whole and resurrected by an evil space necromancer of Chaos, I'd say "OMG..."