I agree that having Johnathan around would have been better given his previous ties to the Buffy and the others. However, if the roles were reversed, then it would have been Johnathan who killed Andrew, and I like to think that among the trio, Johnathan was always the one with the most heart.
I didn't mind Andrew. He was annoying at times but I did like that he was a full-on nerd and added a much needed lightheartedness to season 7 in a role that Xander had almost lost by that point. He killed, yeah, but what was he supposed to end up doing, go to jail? I think in the world of the mystical, doing that just wasn't that possible. I don't think he got away with murder, he did have remorse and he did end up fighting for the good side in the end. Even though Buffy lived in the real world, she also lived in the mystical and fantastical one. Regular rules of right and wrong, of the law, just didn't apply as well and I was willing to overlook it.
I suppose his redemption would have been better served if he had died fighting to help the others, dying instead of Anya but...I don't know, the fact that he does live despite the fact that he should have died does make things a lot more interesting.