It will work better than you think it will. People will endorse comments they disagree with just to get the opportunity to rebut them. Users don't debate things on HN to right the wrongs of the universe; they debate because debating is (or can be, when the comments aren't horrible) gratifying.
No it won't actually. What you described might be the 1/1000 of the cases. Most of the times
when someone tells an unpopular truth that is hard to debate, it'll be more gratifying to just
silence that unpopular truth. And that is called human nature.