Allow me to preface this by stating that I, obviously, believe murder is both intuitively and objectively wrong. On what basis do I claim this? I assert that morality is objective, grounded in God. By objective, I mean independent of people's opinions. Therefore, I see the statement "murder (or rape, genocide -- etc) is wrong" as true as the statement "2 + 2 = 4" (or is it 5? I'm no bueno with math, mister).
Now, given naturalism, there's just no way you can derive moral values or duties from a test tube. You cannot get an ought from an is. Science is morally neutral. It follows immediately that moral values and duties don't really exist. They're just illusions of human beings. Even if the naturalist is willing to go beyond the bounds of science, why think, given a naturalistic worldview, that human beings are morally valuable? On a naturalistic view, moral values are just the by-product of biological evolution and social conditioning. Just as a troop of baboons exhibit cooperative and even self-sacrificial behavior because natural selection has determined it to be advantageous in the struggle for survival, so their primate cousin Homo sapiens exhibit similar behavior for the same reason. As a result of sociobiological pressures there has evolved among Homo sapiens a sort of "herd morality," which functions well in the perpetuation of our species. But on an atheistic worldview, there doesn't seem to be anything about Homo sapiens that makes this morality objectively true. If I we were to rewind the tape of human evolution back to the beginning and start anew, people with very different set of moral values might well have evolved.
For us to think that human beings are special or that our morality objectively true is to succumb to the temptation to speciesism, an unjustified bias toward one's own species. So if there is no God, any basis for regarding the herd morality evolved by Homo sapiens as objectively true seems to have been removed. Take God or objective morality out of the picture, and all you're left with is an apelike creature on a speck of dust beset with delusions of moral grandeur.
Certain actions such as incest or rape or murder may not be biologically and socially advantageous and so in the course of human history have become taboo, but that does nothing to show that rape or murder or incest is objectively wrong. The murderer or rapist who goes against the herd morality is doing nothing more serious than acting unfashionably.
So while it would obviously be inconvenient to the person being murdered to have his or her life taken away, there's no reason, given naturalism, to see murder as objectively wrong. While most people would obviously rather live than die, this gives us no reason to see murder as objectively wrong if morality is seen as nothing but a man-made construct. While a society may not function too well with a bunch of murderers (or if murder impedes an idea of progress), that doesn't mean that murder is objectively wrong.