I thought the comment was exactly as negative as it ought to be. The author is an idiot and he should be lampooned like one.

Not the issue. It isn't that you owe better to the author; it's that you owe better to this community if you're posting here.

What exactly is wrong with the first and last bits? They're a bit harsh, but not gratuitously so.

What's gratuitous is of course a matter of interpretation. But I'd say the first bit breaks the site guidelines by calling names ("reeks") and being a low-information rant. The last bit breaks the guidelines by being a personal attack.

Try reading just the 4th para ("Yes, the events happen") in isolation. Do you see how much higher the signal/noise ratio is there?

The first bit ain't attacking the author, though; it's saying the article reeks of those things. That's a very common and reasonable way of expressing that opinion, and it falls short of being ad hominem. Also, at the risk of focusing too much on semantics, "reeks" is an adjective, not namecalling; it's a colorful adjective, but - again - one very commonly used even here on HN (at least in my observation; I'm sure you've got better data on that front).

The last bit is indeed directed at the author, but in the context of the comment's overall point ("Vice journalists earn a living by twisting pure things to make them easier to ridicule") it's spot on and doesn't really cross any lines IMO.

In other words: pulling those bits into isolation and judging them on their own is disingenuous to the commenter's point. Same goes for the remainder of the comment being evaluated without those two bits. The whole comment is a single unified whole, and ought to be treated as indivisible; failure to do so leads to these sorts of misinterpretations.