The principle of charity, however, does not apply here- the evidence clearly shows that human beings throughout history have truely believed that some things are morally wrong and some morally right on a level more than preferences, even if this is not in fact true.
Philosophy typically involves taking folk notions that are important but untrue in a strict sense and constructing something tenable out of that material. And I think the situation is more ambiguous than you make it sound.
But it is essentially irrelevant. I mean, you could just go back to bed after concluding all moral statements are false. But that seems like it is ignoring everything that made us interested in this question in the first place. Regardless of what people think they are referring to when they make moral statements it seems pretty clear what they're actually doing. And the latter is accurately described by something like subjectivism or quasi-realism. People might be wrong about moral claims, but what we want to know is why and what they're doing when they make them.
A typical person would be insulted if you claimed that their moral statements referred only to feelings. Most philosophical definitions work on a principle which isn't quite like how ordinary people see them but would seem close enough to an ordinary person.
There are a lot of uses of the concepts of right and wrong, not just people arguing with each other. Ethical dilemnas, people wondering whether to do the "right" thing or the "wrong" thing, philosophical schools (think of the Confucians, for example, who don't define 'right' or 'wrong' but talk about it a lot). Your conception only covers one use.
There seems to be a widespread impression that the metaethics sequence was not very successful as an explanation of Eliezer Yudkowsky's views. It even says so on the wiki. And frankly, I'm puzzled by this... hence the "apparently" in this post's title. When I read the metaethics sequence, it seemed to make perfect sense to me. I can think of a couple things that may have made me different from the average OB/LW reader in this regard: