Conflict is essential to human life, yes, but that doesn't mean everything that people do in conflicts is ok. Quite the contrary. Milner's point is that we need to figure out how to stay with and endure conflictual differences without resorting to the things that make conflict worse. In internet forum terms, that means not resorting to snark, flamebait, swipes, and the other things that the HN guidelines ask commenters not to do. Allowing the tension of differences without lashing out is, I think, the heart of tolerance, and is what gives a chance of finding solutions other than endless battle. Milner's point about that seems to me profound, original, and directly relevant to HN—that's why I put it in my About box.
I don't think that the people who flagged your GP comment did so because they have a problem with freedom of expression. I know the users who flagged it. I think they were simply, and rightly, reacting to the flamebait in the comment. It shouldn't be hard to understand why posts like "Y'all have no idea how fucked the US is and you're all cheering like it's not happening" get flagged here.
Btw, I did respond to this part of your argument already, when I said "If you want to make a case for yourself as a principled poster of dissident views, you need a better foundation to stand on than the GP comment and the other ones I linked to, which are just typical flamebait of the sort we're trying to avoid."
Have I answered your critique now? I'm not asking if you agree with my answer—I'm sure that is too much to hope for—but I'm curious to know if you at least feel like you got a response.