Elaine going back to being Justin's lackey -- part of the Sith Bathrobe Brigade -- would be agony... It would throw him straight back to the torments of the original betrayal, the agonies of those events. "The first girl he ever everything'ed" is still(again?) secretly betraying him with Justin in pursuit of power.
It would hurt him, sure, but not any more than if she went to the dark side by helping someone else. The only difference would be that he would probably be more disgusted with himself for not having worked it out.
Having not-actually-killed Justin? Actually may not seem like a big enough feather on the scales of justice. There's plenty of warden-sword fodder in Harry's past, even without Justin's death.
I weigh things differently. Killing Justin was, in his opinion, what made him bad. Everything else just confirmed it. To me, that would seem to imply that killing Justin did more damage and was a greater source of pain to him personally, regardless of the objective measure. It's like Harry was shoved down a flight of stairs through a window, and ended up with bruises, lacerations, and a broken collarbone. All of those things hurt, but a broken collarbone hurts worse, and if it suddenly isn't broken anymore he's still going to feel quite a bit better even though he's still injured.
However, I have revised my opinion. I no longer believe that finding out that Cowl is Justin would make him feel better--I believe that he simply wouldn't accept it as true. As I posted earlier, there's no particular reason for him to believe it, and several extremely good reasons not to. Furthermore, he lives in a world where not only is shapeshifting a thing, but it's known to be used for extremely detailed impersonation.