I can think of a lot of 'disgusting and outrageous' things games have made me do, but the only time I've ever been genuinely disturbed was in The Last of Us, when it makes you kill the surgeon. I could go on a multi-paragraph rant about how damn impressive i think TLOU's narrative structure is, but to give a TL;DR:

For me, that scene was the exact moment i realised Joel had become the bad guy. That the game's primary narrative focus had been to manipulate my perspective, to make me empathise with Joel through Ellie, and to use that empathy to make me rationalise his action as him just looking out for her. By the time you realise how deep down the rabbit hole you've gotten, how selfish the actions you're rationalising really are, it's too late. By then the game has stopped pretending you have a choice, has made you point a gun at the defenceless surgeon, and has made you kill him. The worse thing is though, even now, i still want to rationalise it all away. I still want to shout a big "fuck you!" to TLOU's world, and give Joel a big thumbs up for being a selfish piece of shit, and putting his need for Ellie above humanity's best hope for a brighter future.

I know not everyone will have gotten as invested in the story as i did, but for me personally, TLOU is currently the peak of video game story telling. Games have made me feel happy, sad, scared, etc, but never as conflicted as TLOU left me. 

The white phosphorus bit on Spec Ops: The Line. Man that was brutal..

I'm not sure I'd say Joel was a bad guy, or he had become one at that point. The only thing that warped throughout his adventure was his stance towards Ellie, whom he started considering as a daughter of his own, either to cope with Sarah's loss or to finally move on and start anew (probably the later since he doesn't have any trouble talking about Sarah at the final chapter, unlike what happens in the dam). Joel was never a "good" guy, he was a mere survivor who did what he could to get along this new world. This is often referenced throughout the game, whether it comes from Tess or from Ellie (the later remarks Joel's skill to know about ambushes, on which he remarks he's been on both sides). I don't really consider the game manipulated the player's perspective in any way. The signals were there all the time. The philosophy, the attitude. How he react to others. Joel was well-established from the get-go, and the only non-established (but predictable) part was him getting along with Ellie sooner or later.

Ask yourself this. Why wasn't he more angry at Henry after he left him to die? Because Henry says "you would have done the same", and Joel agrees.

Joel isn't a selfish piece of shit. Joel is a man deprived of everything. He doesn't owe the world anything. You can't (or shouldn't) call a man selfish for trying to save what little he has left (Ellie), since the world being saved wouldn't give him that little thing back (quite the opposite). He already showed doubt after the giraffe scene. He asked Ellie to leave and just be them together. Ultimately Ellie was robbed of him, not even a goodbye or anything, so you can't expect Joel, a hardened survivor who found a new reason to fight for, to just put it aside and go back to his old place where he has nothing anymore (no Tess, and after all that time he probably doesn't give two shits about the stolen weapons anymore).

The surgeon might have been innocent, but he was standing between him and Ellie with a scalpel on the hand, threatening Joel. In this kill or be killed world, that's was more than enough to get yourself  killed, even if your intentions were pure. He's not the first nor the last that would succumb to such fate.

-snip-

I actually tried to have the surgeon kill me at that point in the game (but he wouldn't). It took a long time before I accepted that I had to kill him to move forward.

Be it pushing a man to be burnt alive in order to advance