The first game I thought of upon reading the title of the article was 'Shadow of the Colossus'. There's a particular boss about half-way through the game who resides in a small secluded garden and the process of defeating them involves tricking them in to ramming over columns etc. until they are trapped.
I have a strong memory of being 12 years old, lying awake at night with the melancholic feeling this article describes, with the realisation that those beasts never did anything to me and I was essentially going out of my way to trick and slaughter them.
No other game has invoked that feeling in me since. It's a very special game. It remains one of my favourites and a stellar example of what the medium can achieve.
When I tried to play SotC, I got too distracted exploring the world to actually go after the bosses. Should blow the dust off it and try again one of these days.
To me, these reflections upon my aggressive and violent behavior in a game are much more impactful than games that put me into dilemma situations, where you are already presented with a nicely arranged moral problem in the moment.
These are two distinct techniques and I feel the latter almost always failed to impress me much, while the first one is where I feel caught, even shocked by myself and the cold-bloodiness to (virtually) follow any suggestion to kill.
The first game I thought of when reading the article was Shadow of the Colossus, mostly because the article opens with a screenshot of the game and talks about it in detail.
I appreciate the honesty of recognizing that you commented without reading the article, but could you not? Your experience could have added so much more had you placed it in context with the rest of the article.
Shadow of the Colossus came out around the zeitgeist of when people really started earnestly debating if videogames were art. After that game there was no more debate.