It is mainly about the let the world burn mentality and what he did to Molly. Harry breaks himself about killing Susan but that was not the point, Susan wanted it and for good reasons. I do not think the killing of Susan was considered evil at all. There was not that much attention to it given in ghost story as a thing Harry had to learn about.
Personally, I've always thought Changes was about Harry's personal chickens coming home to roost—the consequences of all of his decisions between Storm Front (really, everything he'd done since Justin) and Turn Coat. The friends (and enemies) he'd made, the Big Things he'd done, the cataclysms he'd stopped... all of it came to a head, and he was left with a terrible situation. We know how he "resolved" that. But, in my opinion, the plot of Changes was still very much happening with Harry; it was his own, personal comeuppance. Naturally, Harry's comeuppance isn't focused on making
him suffer. It's centered on making someone he cares about suffer, because that's what would suck more for him. The fact that the heartripper ritual would kill him too almost doesn't even matter to him.
Ghost Story was about the impact of Harry's decisions (including the genocide and subsequent suicide) on everyone
else. It's about showing him the debris field of him bullrushing through a dozen or two major events and mistakenly believing that
he was the one paying for all the damage he caused. He paid for a lot of it, but not all of it; others wound up trying to cover the remainder of the bill. And now he wasn't there to even help...provide... cover for the dine-and-dash? The metaphor is getting away from me.
Anyway, I see Changes and Ghost Story as mainly illustrating two sets of consequences of The Decisions of One Harry Dresden, Mad Wizard and Defender of Little Guys: the first for himself, the second for everyone else.
On the microfiction: this kinda ties in really well with my thoughts on the Defenders of the Bean. Molly is expanding Harry's reputation tremendously here. Makes me wonder what kind of impact that's going to have later on, if any.