It's funny that I agree with you and my first instinct was to upvote (and I did). But I can justify that as being because "it's an interesting point that I think more people should read."

I think people will always want to be able to express whether they agree/disagree with things, and if you provide good/bad content buttons but not agree/disagree, a lot of people would just abuse the good/bad content buttons which would largely defeat their purpose. I agree that the ratio of agree/disagree should have no bearing on the order that threads are displayed. So perhaps the purpose of agree/disagree could just be to give users a way to express their opinions without compromising the good/bad voting, and maybe even allow users to find old content they agree/disagreed with.