Honestly, one of the best games as of recently that I've played which includes a couple of hard, thought out moral decisions is "Silent Hill : Homecoming". It is a survival horror genre and although there is a lot of combat, if you have actually played through any other games in the series, you'll know they're all morally deep and a bit sadistic but also deep. I've played the entire series all the way from the first Silent Hill, and besides 4 (which is an off-shoot with it's own story), they all intertwine, follow each-other yet involve different people. But they all have very moral decisions you must make. In the new one, which is the 5th one in the series (homecoming which I mentioned earlier), the decisions you make will change your ending, as in the other ones, but the new one hit home the most.
However, I wouldn't recommend them if you can't handle rather disturbing games. Because unlike games like Resident Evil, Silent Hill focuses on more disturbing and macabre things than a typical zombie shooter. For instance most of the monsters are extremely disturbing and horrifying, and some of the things that go on in the game really creep you out.
But with the story there is almost no comparison. The whole series is about moral decisions, and includes a lot of hot topics. It's all focused around a secret religious order in which people think they're doing good and kind of have this sense of "sacrificing one for the good of all". Playing through the entire series would be my suggestion, but even picking up the newest one won't leave you out of the dark for too long, since they describe things rather well. But make sure you pay attention to the storyline and never ignore cut-scenes or blow through dialogue, or else you don't get the full effect.
Not only that but all of the Silent Hill games have been graphically and playability wise good for their time. But yeah, just prepare to be disturbed, especially with the two major points in the new game where you must make a decision. I won't ruin the story but one involves ending suffering before death or being too moral to cause death yourself, but allowing pain to happen, and the other involving forgiveness for a lifetime of guilt.
Yeah, sorry I kept going on but I had to kind of describe it to give you the effect.