Why do you say the HN community is toxic with respect to these topics? For example, all of the top comments on this article are in favor of YC's announcement and supportive of what they're doing.
And it stinks that the HN moderators' reaction to this issue generally seems to be to brush it under the rug. Almost all meaningful discussions on this topic are quickly flagged off the front page.
You don't solve a problem by pretending it doesn't exist.
Moderators don't flag stories off the front page, users do. The most common moderator reaction to threads on this topic is to turn off the flags, ask people in the thread who are violating the guidelines to please stop violating the guidelines (or ban them), and sometimes post a preemptive top comment asking potential commenters to please not violate the guidelines.
This is a community site and the members of this community are responsible for their own behavior, including how they relate to the community. This is why there are user moderation tools like voting and flagging.
I realize the mods don't control the flags. They do however know that flagging is an issue when it comes to these topics. They could do more to facilitate the discussion of these issues. They already do dictate behavior in a number of other ways (e.g. personal insults are one thing that results in heavy moderation).
EDIT: A prime example is that this post is currently 5th on the HN front page and has roughly triple the points of the 3rd and 4th items on the front page in roughly half the time. That means this post is almost certainly being suppressed with flagging. Will the mods do anything to protect this post?
Could you please email us at hn@ycombinator.com with suggestions? We're always trying to improve quality and it's helpful when users let us know what their ideas are.
Edit in response to edit: Yes, moderators (me) turned off the flags on this post. Points can't be compared directly between stories because that's not how it works.
Here's one of many possible improvements: keep track of stories that had to be "rescued" from being flagged to death, and anyone who flags more than one of them loses both flagging and voting privileges.
Here's another: if you had to turn off flagging on a story, turn off the comment-based heuristics at the same time.
Here's a third: rethink the comment-based heuristics, and consider what kinds of discussion you're trying to curtail.
The existing mechanisms y'all have been using (suppressing posts with many flags or with many comments) seem like they just don't work at the current scale of hacker news even if they did when it was smaller. In particular, the fact that the system(s) were exploited to push a YC survey down on the front page is a bummer - I have no idea where else I'd find out about a YC survey other than YC's website unless I rely on some site like techcrunch to publish a writeup about it days later. (Where will they see it if it gets pushed off hacker news?)
Once a story hits a certain vote threshold it probably needs a reprieve from some of the automated filtering mechanisms, at the very least. Disabling comments in response to flame wars would be much better than suppressing the story itself. Flagging seems good for fighting link spam, but a flagged story with many comments would suggest an intense (and not necessarily heated/flamey) discussion that has value and would naturally attract flags from people with an axe to grind.
Those alternatives should probably be advertised better than just that tiny link in the footer.
If you're only interested in YC news specifically, you can also subscribe to https://blog.ycombinator.com/feed/ . Most of the articles there don't ever make the front page, I think.
Stop penalising stories based on the behaviour of users in the comments. If users can't be trusted to discuss something, disable comments on the story instead. This site isn't purely a mechanism for enabling discussion - it's also one of the primary ways that members of the tech community can become aware of issues, and algorithms that prevent sensitive topics from being visible because they always trigger pointless arguments in the comments don't provide benefit.
I don't have access to your ranking algorithm, so I can't tell you how to fix the issue with this post being ranked lower than the 3 posts directly above this on the front page that are all older, have less votes, and one has more comments. I also don't have access to the data you have on flagging and what type of posts get flagged. I imagine there are ways to identify controversial topics like this that receive a high amount of both votes and flags. Do those posts deserve special protection? Maybe you look at how a user uses their flag permissions. Should a flag from an infrequent flagger have more weight than a frequent flagger? Can you identify a flagger who uses the flag inappropriately? Should there be some type of shadow banning on the flagging functionality? These are all things I would want to explore if you are legitimately looking to allow these type of important conversations the flourish on HN.