Any reason why HN source code is not published? The best I can think of is not to let people see the penalizing behavior, but having an open standard might actually help it improve rather than keeping it as a hidden secret that slowly gets discovered by independent malicious parties.
I wonder if it would be possible to split HN (or any other HN-like site) into two halves: one would handle the actual storage of posts and comments, and another would handle the scoring, ie the order the comment tree branches appear in. Then we could have multiple of the latter, competing with each other on the scoring alone, with the actual content being common.