That's wrong. Both the flamewar detector (a.k.a. the overheated discussion detector) and user flags do that, and there are other software mechanisms that do it too. For example, if a story has been on the front page for more than (IIRC) 18 hours, it gets an automatic downweight unless we manually override it.
Also, keep in mind that user flags affect a submission's rank long before the [flagged] marker appears.
Meaning if someone were to theoretically get a real time feed of HN submissions, and flagged articles that they didn't want seen as well as messaging a group of friends to do the same thing. Do you have protections for this type of behavior that would prevent this person from having undue influence on what can and cannot have a chance at being seen by others?