These sorts of events are tricky on HN, all the user can do is flag flag flag and hope you or others like you (mods) will sort it all out and give the front page its one thread on the topic, if we don't the front page will be consumed and the community will die. But we can't always rely on mods, you have lives and have to rely on certain pragmatism, you have to wait and see how the community reacts/events unfold to see if something should get a thread on the front page or risk the consequences. And I think you did weigh in but vouching on a single thread may have won out against the flagging, as it should. So I gave the thread a chance and started reading.
One of the only changes I think HN could use, is mods being able to make a post in a thread that can not be voted on or replied to but will remain top post and simply stating that the community has ruled and this submission will live but every related submission will be killed as a dupe until the thread dies. But that would be very difficult to do without being accused of having an agenda by one side or the other.
Part of the reason I avoid becoming too much a part of sites like HN is because I fear being asked to be more than a user. I do not envy your position but I appreciate all you do.