I'm actually glad that this got brought up, because it's been something I've been thinking about for quite some time. In the end, I don't believe that simply setting out to upset the player and then accomplishing it by easy means (such as vivid depictions of violence) can be classified as "art", even though it's a common defense. Art is meant to be evocative, yes, but simply fishing for a reaction, any reaction at all, and obtaining them by any means necessary isn't evocation. It's simple shock.
Saying "I want to push people out of their comfort zones" and then making them, the player, torture people to death... Well, you've achieved your goal in discomforting the player, but to what purpose? What are you actually saying? You've solved an equation, but that's all. With the nebulous state of "games as art", of course, people will call anything art just to be seen as an advocate of the movement -- but a critical eye is necessary.
Let's say I'm a performance artist. I make it my goal to be "seen", so I go around in a scary mask screaming at people. By my own standards, I've succeeded, but there's no denying that I've set awfully low and broad standards.
It is not humor or joke. He really did insert a nail through "it" and he suffers from it greatly and it brings him closer to god and he thinks by sharing pain with others and making them feel great pain helps take them to god as well. It is mentioned the nail will most likely kill him, even if he removes it or keeps it.
If this was your intention, then your presentation of the event was almost criminally lacking. This isn't the sort of thing that you can put in author's notes later -- it has to be apparent from the work itself, speaking on its own behalf. Without you speaking for it, the event seems as if it can only possibly be a joke, or a quick shock. There's none of the gravity that you're attributing to it.