Surely it us missing just because many have flagged it. But that's far short of silencing it.

I imagine—but then that is just the HN community silencing it. Maybe flagging should have some different kind of weighting?

I think discussions should be made immune from users flagging them if they have more than a certain amount of comments (50? 100?). If it's a problematic topic, then the administrator(s) should be able to flag it if they deem it necessary.

That would surely suffer the cobra effect.

It is not silenced.