Well, it is my reading of Sam Harris' reading of Haidt that suggests Haidt's argument is unsound:
Emotions are a bigger factor in our determination of what is right and wrong than reason.
Emotions are subjective.
Therefore right and wrong is subjective.
There may be a transmission error between my reading of Harris or between Harris' reading of Haidt but all I am showing is that Harris thinks Haidt's work doesn't demonstrate that arguments made intractable through heavy emotional investment shows that there is no fact of the matter. It is merely one objection that he is shooting down. Harris may have chosen to show this by substituting what is right and wrong with the truth about 9/11.
Emotions are a bigger factor in our determination of the truth about 9/11 than reason.
Emotions are subjective.
Therefore the truth about 9/11 is subjective.
So, if my reading of Harris' reading of Haidt is correct then I think it is fair to say that Haidt's objection fails. It doesn't, of course, mean that there aren't more successful objections.
If that is his argument, then I can only point out that he has mangled it in my estimation.
In fact, I think he has sidled his way into an equivocation fallacy.
There are forms of reasoning that do not depend on emotion; we call them mathematics/calculation. It's what our current iterations of computers do.
For human reasoning to function, however, emotion must play a role, but it plays a slightly different role in different types of reasoning.
So, for instance, the reason why we engage in discussions about 9/11 is determined by desires and motivations, but the reasoning process itself is best left to arguing data not determined by emotional factors. His argument about how truthers go about their business supports Haidt's position that folks have a marked tendency to rely on ascertainment bias in their arguments; and emotional input is the primary reason behind it. When it comes to what actually happened on 9/11, however, I will repeat, there is a set of data that is explained better by one and not the other theory. ETA: That a group of people flew planes into several structures and there is no actual evidence of explosives in the rubble, etc. are simple facts. They are not determined by our emotional involvement in discussing the process. Granted, the importance we assign those facts is determined by our emotional involvement, but that is part of the equivocation as I see it.
When it comes to moral reasoning, however, we have no recourse but to rely ultimately on emotion/motivation/desire/feeling. Morality does not exist without values and values do not exist without desire/feeling. In that sense, feeling is the very basis of all moral reasoning in a way that it is not for other types of reasoning -- we only think about 9/11 because of our feelings about it, but we should not think about it using our feelings about it as the primary mode of intellectual input. Feelings are, by their very nature, the primary input for moral thinking, though. ETA: Or, in other words, emotion/desire/motivation/feeling constitute the 'facts' in moral reasoning (as opposed to reasoning about occurrences in the world that many people can see where the facts do not depend on emotion).
So, folks might make the mistake of interjecting too much emotion into their appraisal of 9/11 facts, but it does not follow that subjectivity being the improper approach in that instance translates into a mistake in moral decision making. Morality simply is another fish.