I don't think there's any way to get perfect or even very good balance here—the instruments we have are too crude.
It's one thing to downweight a post that duplicates content on the front page. It's another thing entirely to downweight a post that tells the other side of the story.
It's easy to argue for a different approach when you care about one story in particular, but we need an approach that generalizes well. Front page slots are the scarcest resource on HN, and we have a responsibility to keep them diverse. If we didn't do that in general, I guarantee you that many more readers would complain.
Btw, this isn't a question of taking a side in the dispute. The original NYT article received more attention on HN than any of the pro-Amazon responses did. We weren't anti-Amazon in that case and we aren't pro-Amazon in this one.