This is an ordinary case of two regular phenomena: (a) a major ongoing topic; and (b) negative stories about anything YC-related. We deal with them as follows:
(a) We deal with a Major Ongoing Topic (MOT) [1] by downweighting follow-ups [2] and reserving frontpage slots for stories with Significant New Information (SNI) [3]. This is the approach we worked out back in 2013 after the Snowden debacle (I don't mean the debacle involving Edward Snowden, I mean the debacle involving Snowden-related stories on HN's front page). It has held up well in the years since. It requires a judgment call about what is/isn't "significant new information" but that's usually not too controversial and in any case it doesn't matter whether the information is positive or negative, nor who it's about.
(b) We deal with stories that are negative about something YC-related by moderating less than we normally would [4]. Note the word "less"—i.e. we still moderate those threads, using the standard principles we normally apply. We just do it less when the story is negative about YC. That's another approach that has held up well over the years.
It's fairly rare that we get a MOT which is also YC-negative. In such a case we're going to get complaints no matter what we do: if we apply the normal principle of downweighting follow-ups, people will accuse us of censoring the story; but if we don't, people will complain about the frontpage being filled with follow-ups.
[1] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
[2] https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que..., because https://hn.algolia.com/?dateRange=all&page=0&prefix=false&so...
[3] https://hn.algolia.com/?dateRange=all&page=0&prefix=false&so...
[4] https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu...