I don't think it's Murphy's time yet. If she dies at all, it'll be after we get a sense of their dating relationship for a book or two. It's too soon—both in terms of amount of story told and in-universe time between entries (Peace Talks is six months after Skin Game). She'll probably still be in physical therapy/rehab after the beating she took in Skin Game, likely sidelined and unhappy about it. If Jim does decide to kill her off, I think it'll be the event that sends Harry into self-imposed exile, like the beginning of Summer Knight, but, you know, full retirement. I'm talking last Case File book. Harry's called out of retirement for the BAT. That's my guess, anyway.
Narratively speaking, I could say Ebenezer will bite it, but after he delivers ten to fifteen pages of crucial exposition. Background information on the Council, the Outsiders, Justin—whatever will push the metanarrative forward into the next cycle of books.
Personally, I think that Ebenezer will die at Ground Zero, surrounded by hundreds of charred corpses. Hmm. That could work for Peace Talks, actually. Harry could get sucked into the alternate timeline right at that moment, saving his life (and also making sure he doesn't have to hang around for the cleanup).