When a negative story about YC emerges and generates a lot of comments so it gets pushed off the front-page and they just say "shame but its just automatic flamewar detector, <shrug>". I'm sure they think they are clever but it just erodes trust over the long term.
Trust me, there's no room for feeling clever in this job.
What do you think about leaving the penalties open for user customisation? I find its more miss than hit as a flamewar heuristic and would prefer to scroll past real flamewars rather than know that popular topics are suppressed.
It's literally the first rule of HN moderation that we don't suppress stories that are negative about YC or YC startups. More precisely, when stories like that appear, we moderate them less than we usually would. The reason is precisely what you said: long term trust is the most important thing. Also, before being moderators of HN, we're users ourselves, and wouldn't want the site to be moderated that way.
Sounds like an odd cough algorithm.
When people see something they don't like, they don't think, "Well, any even-handed system will put up things I don't like sometimes." They think: Bias! Outrage! And some rush to "J'accuse!". In any large group this will happen to quite a few people every day (sometimes the same few!), and it takes 100x as much effort to responsibly respond to the j'accuses as to fire them off in the first place. This would amount to a DoS attack on resources that we could otherwise use to make HN better.
Therefore our goal should not be the impossible one of placating everybody with a litigious bee in their bonnet, but (a) being able to say "no, we don't do that" in good conscience, and (b) retaining the good will of the community as a whole. Actually we like to help users with bees in their bonnets too, but to think it can always be done leads to madness.
We're toying with adding vouch links so users can vouch for a story they don't think should be marked as a flamewar. That's something that might improve the quality of HN.
Makes sense about releasing more stats - how about internally then? Could you take a look at the number of pro- and anti-YC stories that you've turned the system off for and see if it seems unbiased? Often it's easy to judge each story one by one and think you're being unbiased. But we're all biased. Going back and checking those stats may reveal something you didn't think was happening. Or not. Not as any kind of placation, but more as an internal quality check so you know you're on the right track.