As for Valentine...having her get blown away by Kira certainly denies closure to Shinn, who is a much more important character than Kira in this story anyway. Athrun had written Kira off entirely by the end of "ETERNITY," but Shinn said it himself when he said he knew he'd be haunted by their unsettled score if he just let Kira go--and as far as he was concerned, Kira was beyond salvation anyway. It's not as though they were going to come to an understanding, anymore than Amuro and Char did in the end. And Shinn is not a particularly forgiving guy to begin with. He might have forgiven Rey for his manipulations, or at least stopped caring about it, but that was after he'd killed him.
And as for the rest...
There are plenty of characters over the course of this entire story who have doubts but never get to act on them. Rey, for example, was constantly pushing himself back onto the path of vengeance against Shinn; numerous ZAFT characters like Glasgow and even Rudolf were willing to admit that they were doing horrible things; Kara eventually came down from the height of Natural-hatred, but she hardly chose her fate and certainly didn't enjoy it.I find it slightly suspicious that Kira is more or less the sole exception to this.
Kira had doubts but never let himself act on them. Plenty of people in actual history have done that. To better use an example I cited earlier in this thread: Adolf Eichmann. Hence, the difference between Kira and Sven is that Kira never actually chose his better nature. And despite all the people who gave their lives trying to get him to do so, in the end, he still had to choose it, because you can't force someone to make the right choice. That he didn't, and thus that those people died trying to save a man who was already dead, is the tragedy.
To have him suddenly realize that he's been wrong about everything at the last minute would be the kind of ass-pull that people accused me of doing in making him turn to Rau and Valentine in the first place. I'm not sure why one ass-pull should be okay but another isn't. And not to mention, it cheapens the sacrifices those previous characters made because it wasn't their sacrifices that did the trick, it was a magical epiphany at the last minute. Like I said, I worked with Kira as I had altered him, and how I altered him was in retrospect not that great, but you're still trying to apply Kira as he existed in the animation to Kira as he exists in this story, and they are obviously two different characters.
That really gets to the heart of the matter. To be honest, I think you are letting your being a huge Kira fan get in the way of your opinion, because you're making him out to be a much more important character to this story than he really was. You're acting as if the moral arc of the entire story rested solely on his redemption; it didn't, and never did, or else there would have been some motion towards redeeming him, and there wasn't (not to mention we would've seen a lot more of him). So Rau doesn't really win any sort of victory, because the battle was never over Kira.
Besides which, you're also making the mistake of assuming that Kira's moral story is the only one that matters. If you act as though Kira is still the main character and invest in him the ultimate moral meaning of this story, then yeah, it looks pretty grim--but you have to ignore a hell of a lot of stuff to get there. So Rau might have been right about Kira, but so what, he was wrong about a whole raft of other characters, and being right about one person hardly proves his point when he was wrong about so many others. He thought he could plunge people into darkness and despair and they'd never find their way out. Some didn't, but others did, and that others did proves him wrong.
Emily proves that most of all, not by misinterpreting his message, but by going through darkness and despair herself and coming out on the other side still able to pursue happiness. And that works out--because she's the main character, not Kira.
Man, I write a happy ending and I still have people thinking it's grimdark.