There were no real long-term consequences for killing multiple innocent civilians in the game; indeed, some amount of "collateral damage" was expected and built into the mechanics of the game so the player wouldn't be unduly punished for a few stray bullets. But the resulting freedom of choice actually had a much more profound effect on me than any cutscene of being arrested and hauled off to jail would have.
In 1985, noted philosopher Michael Ruse wrote an article entitled "Is Rape Wrong on Andromeda?" In the article, he postulated that if intelligent alien species existed on other planets in the universe, they might have different notions of morality than our own. Taking his cue from the growing field of what is now known as evolutionary psychology, Ruse argued that much of what we consider moral is shaped by hundreds of thousands of years of evolution and natural selection. Indeed, many biologists today believe that a variety of beliefs and behaviors like justice, fairness, mutual cooperation, reciprocal altruism, proportionality, inclusive fitness, kin favoritism and even the instinct to protect children all evolved from basic biological behaviors that made those who followed such principles more likely to survive and pass those values on to their offspring.
So, it stands to reason that extraterrestrial morality would be shaped by a set of different environmental pressures, and that an alien's resulting moral code may be quite different than ours as a result. In a society where simple biology dictated that females only came in heat one day a year and were responsible for all of the child rearing, the males may have no choice but to engage it what we would consider rape simply to ensure the survival of their species. As their species became sentient, a whole complex system of morality may arise to justify such behavior in a way that most of us cannot fully fathom. This is not to say that such behavior is either right or wrong in an objective moral sense (assuming you even accept that such a thing exists), but simply that it is, for lack of a better word, appropriate behavior in that particular context.
How does this relate to games? To put it simply, the environments we experience inside games are other worlds, and many of the avatars we play in them are essentially alien creatures who may seem human from time to time but are not entirely so. Their actions may not always map one-to-one with our sense of reality, and something that is not acceptable in our world may be entirely appropriate within theirs. Of course, by this I do not mean to justify or endorse in any way the harassment or "griefing" by one player of another in a multiplayer game; those are actions with real-life intent, directed at another real-life person, with real-life consequences. But within the context of the reality of the game itself, it may be entirely acceptable for a warrior to attack a seemingly unsuspecting centaur or for a hoodlum to shoot a hooker.
Back in March at the annual Game Developers Conference, I sat in on a roundtable discussion of the issue of sex in games. One of the participants was a woman who worked for a media watchdog group whose primary concern was ensuring that sex, when portrayed in television or movies, was dealt with realistically and responsibly. While not trying to impose a morality in the sense of advocating either "Yes, unrestrained sexuality is great!" or "No, sex outside of marriage is wrong!" they were interested in making sure that the consequences of having unprotected sex, like pregnancy and STDs, were appropriately shown. At first blush, such a goal may seem quite reasonable, even admirable, to most of us. In recent years, the organization has set its sights on videogames and wanted to advocate these same principles to game developers.