I think what makes this seem so wrong is the callousness involved.
Spike and Anya were both mass-murderers when Buffy and Xander decided to hook up with them... but neither of them had actually managed to kill anyone they knew personally. That shouldn't matter from a strictly ethical perspective, but from a practical perspective, it does matter. Most humans simply don't have the same empathy for the lives of people we don't know, as we do for our friends. That's a survival trait... if we cared so much about every life, we'd never be able to do anything but grieve.
In this case, though, Buffy is getting it on with a man responsible for directing and overseeing the deaths of hundreds of her own friends and colleagues. These are people she knew personally. People who looked up to her, even idolized her. People who depended on her and trusted her absolutely. People who gave their lives to help further her vision of fighting for good. And she responds to their killer by... yelling at him for all of thirty seconds, then giving him nookie.
Yes, I know he's given her some sketchy, unsubstantiated disclaimer about how he didn't really kill anyone even though we saw him do so, yada yada yada. Is he claiming that he didn't direct that army of demons to attack the Scotland base, killing dozens of Slayers? Is he claiming he didn't stand there commanding the army that killed dozens more in Tibet? Or that he didn't give Warren the OK to fire that missile, or Amy to send those demons into the catacombs in Rome? Was it someone else who ordered that lab tech put to death in Mongolia? How much murder does one get away with, exactly, before one stops being on the side of good?
All we really know about him is that sometime between AtF and now, his motto changed from "We help the helpless" to "They're mortal. They had to die sometime."
The fact is that minutes ago, Buffy was very justifiably and correctly accusing Angel of being a mass murderer of her friends, and now she's making out with him and probably more. There is no possible interpretation of reality in which that doesn't disgust me.
Angel coming at her with what basically amounts to "I did it all for you, baby. I did it for us" fails to improve things much, I'm afraid.
So yeah, there's more story to come. I would think there might be some twist that will make it all OK, but really, when has Joss ever been interested in making it all OK?