I'm not afraid of killing characters, including the Boys. I might even enjoy killing the Boys, judging by how every novel I've finished (by myself) in the last decade has ended. Jeez... I have a problem. LOL
As far as the decision to let a character live or die goes, I just try to do what makes the most sense and feels right. Sometimes characters deserve to have a happy endings, and sometimes stories just feel more like tragedies that need to end tragically.
I've never regretted killing a character, but I have regretted the way I've done it. Tracy mentioned Sick as My Secrets (thanks, Tracy), and that's actually the one I have regrets about. I had a plan for how it was going to happen and then changed my mind a few days before I wrote it, and now I think I should have stuck to my original plan. It was going to be a lot less dramatic originally, but that was the point. I just can't resist the drama.
The hardest character death for me to write was probably in Curtain Call. I had a work friend who was dying of cancer at the time, so it hit close to home, but I also think writing that story at that time also helped me deal with my emotions about what was happening to her.
The most devastating death I've read in someone else's story was probably in Swollen Issues III. Even though it was the most believable ending and was probably inevitable, I wasn't necessarily expecting it when it happened, and it was so very sad. The most shocking was probably in an old suspense story called Scared of Reality because one of the Boys was killed in the middle of the story, which doesn't usually happen. But I think that's one of the things that made that story great, and it's one of the reasons I love The Walking Dead, too, even when they kill characters I love. It's more exciting when you have the feeling that no one is safe.