I didn't say anything like "so long as someone is speaking their opinion respectfully and in good faith, it matters not what that opinion is". I try to be cautious about not making grand generalizations like that, or even thinking them. They tend to have grand and troublesome consequences.
What I wrote was narrowly scoped and is mostly an empirical claim: in the majority of cases when users invoke astroturfing/shillage/spying against others in arguments, there is no evidence to support the accusation and usually evidence to refute it. Because this comes up so frequently, it seems there's some sort of bias (probably a universal one, because I don't think we're wired so differently) that causes users to reach for this mud and throw it at other users, even though they have no basis for it other than that person having an opposing view—which is to say, no basis for it at all.
Since there's usually no evidence and yet these accusations are so common and so damaging, the site guidelines ask users not to post them in the threads. At the same time, real abuses exist, so concerned users are invited to email hn@ycombinator.com with links so we can look for evidence.
That was the gist of my comment. The rest was an attempt to plead for tolerance by offering an explanation of how HN ends up with so many posts that can seem disingenuous: it follows from the size and diversity of the community. Humans are not wired for anything that big, and HN is an intimate-seeming place that doesn't feel as large or diverse as it really is, so when views show up that are more than an arm's length away from what one is comfortable with, it activates the circuitry for perceiving enemies and invaders.
If HN is to thrive in accordance with its value of intellectual curiosity, we all need to work on managing that circuitry in ourselves, and not simply jump to where the limbic system would take us. That's really what the call for evidence is getting at. It requires a person to stop, interrupt the mechanical reaction, invoke the slower and more reflective circuits, and then look more closely at what might really be happening. If we could learn to do that as a community, 99% of the accusations of astroturfing, shilling, and spying against other users would vanish. That would make HN a better place, and would also help clarify which cases really do need investigating and taking care of.