There is a perverse incentive here. If commenters can push an article off the front page by flaming, the flamewar detector would actually encourage flaming.
I think that maintaining a community like this is really a dynamic process, so while it's important to make note of bad incentive situations for the future, it's not necessarily the best choice to correct them prematurely. In theory, your reasoning sounds right. In practice, that's probably not happening right now, so the mechanism still serves its purpose with only the (presumably considered acceptable) expected collateral damage.
The important thing with a situation like that is to be ready to kill the feature as soon as people learn how to exploit it. It's one thing to see that it's theoretically exploitable. It's another to actually figure out how to selectively engineer flame wars to make a significant dent in the front page.