Why even allow flagging to influence a submission’s ranking without mod intervention in the first place? Spammy links won’t reach the frontpage anyway (although they sometimes stay on Show HN for a while, so can make special exceptions for Show/Ask submissions).
And how about if a user flag a post, then you might consider making the post completely inaccessible to said user (and if they posted a comment in the submission then set their flag weight to 0 for said submission)? After all, good actors will have no interest in engaging in the submissions they flagged, whereas bad actors will want to attack the submission from all angles (flag submission, downvote comments, post own comments).
> Why not automatically punish users that abuse flagging to censor stories
The problem is with the words "abuse" and "censor". No one can agree on what they mean because it depends on what you think of the underlying story, and when it comes to divisive topics, people have strongly differing views on that.
When the topics aren't so divisive (e.g. Conway's Game of Life on the GPU, or something like that), this is not such a thorny problem. But those aren't the cases that we're talking about in this thread.