Half a million stories get submitted to HN every year. Plenty get moderated in some way; plenty are in some way ghoulish. I'm afraid I don't remember them all; I hardly remember any of them. It feels like you may be putting too much weight on one data point, if you're asking "how you live with doing that" about a specific story from years ago. The answer is that the moderation principles here are clear and we try our hardest to apply them even-handedly.
Incidentally, you can't derive any political agreement or disagreement from the way we moderate HN - we moderate stories and comments all the time that we personally agree with and/or consider important. If you scroll back through moderation comments on HN you'll find that commenters from every political and ideological angle get moderated, because people on all sides break the HN guidelines (https://news.ycombinator.com/newsguidelines.html). I'm not claiming that we have no bias, but certainly we work hard at this and have a lot of practice at it.
If you would please start doing a better job of adhering to those guidelines now, I'd appreciate it.
And no, there is absolutely no way that my second comment was flagged by multiple users within minutes. This thread was long dead by then, and this is on the second page. What you say about the first comment is highly doubtful too, considering it was flagged within one single minute, with one single downvote - and was already also on the second page.
If repeatedly removing the story of an infamous torturer who destroyed congressional evidence taking one of the most powerful technical positions in the country - against loud and polite protestations - is really not remembered by you then you have two big problems. 1, your humanity, and 2, you need more moderators here because clearly you are being stretched too thin. Ask PG for a bit more budget, for the sake of your soul and the people here creating this content.