Man, a lot of Gundam discussion has been happening without me lately. Gotta fix that!
First things first. On the subject of undoing death brought up at the start, as most of you probably know this is a pet peeve of mine. Most of the time, I'm a believer in really meaning it when you pull the trigger. Some other Gundams cheat death too, but these situations are generally limited. There is a place for trick deaths, but if executed badly or done too often you risk losing the tension. As viewers, we should not have a sense of complacency. Don't mistake this as an endorsement of the "kill em all!" approach, though. The essential specific point, perhaps, is that you need challenge and harRABhip for triumph to have the meaning that it deserves.
That said, while Seed crossed the line with Mwu thanks to the special edition's foolish retcon, I don't think it did with Andy. Why not? One, Andy did lose his wife, a person at least as good as he was. By letting Andy live, there's a theme of forgiveness added in that is quite essential. Seed's universe is very much defined by its cycle of violence, and series like Wing and 00 also take this concept seriously. Two, I think multiple other characters demonstrate the issue of good people being on the other side. That's practically the entire tragedy of Kira and Athrun fighting each other in a nutshell, and in time even Athrun's ZAFT pals are put in a better light compared to the start of the series. On the other side, Natarle was strict and generally unlikable but ultimately she was a loyal soldier that was betrayed by the fanaticism of her superior. She didn't deserve what she got; like Flay she pretty much ended up in the wrong place. Ultimately she tried doing the right thing and paid the price, and she was only half successful at best. Azrael dies, but Flay and all of her crew die. That's a bitter trade. Her consequences remain very real.