This is the sort of thing that happens in the Film industry every day. Yes they swear, if there's bad guys and they take a hollywood actress prisoner, no they aren't going to lock her in a castle and wait for Mario to come rescue her. The world they portray is a bad world, and in this bad world, horrible goons will more than likely want to rape stuff. Is it pleasant? No. But let's face it, these "characters" in movies and games aren't supposed to be pleasant. Rape is a deplorable and reviled act, but it happens, and to try and negate it just because a few people don't like it isn't the way forward.
@HybridExtreme nailed it on the head really, video gaming has expanded to be as vast and appealing as the film industry, and if that means that a child of 8 can no longer pick up a copy of Tomb Raider then sorry, but parents will actually have to take an interest in what their children are playing.
Whether or not it's there for shock factor, well again that's not for me to decide. Look at Grand Theft Auto, look at movies like Clockwork Orange, the Evil Dead. These all went for shock factor and it did them well, I may not agree with it, but then I don't agree that releasing a slightly improved call of duty game every 6 months should prompt a billion dollars worth of sales in 15 days... but it does, so guess I'll just have to deal with it.
Remember those old games like Mortal Kombat where you could go into options and turn blood off? Extra work for developers but it's an idea.