Sean Carroll has a fairly brief post over here. He and I are pretty much on the same page, although I should repeat that I don't see the metric problem as the deepest problem. Even if we had a metric and had only practical problems with measuring well-being, there would still be the question of whether it would be a requirement of reason or some such thing that we must act so as to maximise universal well-being.
Or, alternatively, is the claim "You must do X as it maximises universal well-being" just a fact about the world analogous to empirical claims such as "There is currently no rhinoceros in this room"? It doesn't seem to be a logically true claim or an empirical claim, so what is it?
If you say, "Well it's a moral claim" that just seems to show that moral claims are not claims about matters of fact or reason, so how is it binding on us that we must actually act in accordance with them? In very many circumstances it may be a good idea to do so, even by our own lights, but that will depend on just what our own desires, values, etc., actually are.
I don't believe that someone (Alice, say) who acts, on some occasion, in a way that fails to maximise well-being is necessarily mistaken about any matter of fact or acting in a way that is self-defeating or irrational in any other sense that Alice need bother about. We can cheat and redefine rationality in a way that is already moralised, but that will get us nowhere because Alice can just refuse to accept our concept of rationality (why should she accept it if she is not already committed to our idea of morality?).
Sean is correct to insist that the metric problem is not merely a practical one, but one of principle. But the crucial issue goes even deeper than this and would remain even if the metric problem could be solved somehow (by some super-duper neuroscience, or whatever).
I've seen many attempts to get around the problem with morality - that it cannot possibly be everything that it is widely thought to be (action guiding, intrinsically prescriptive, objectively correct, etc.). In my experience, this is like trying to get rid of the bump in the carpet. The bump always pops up somewhere else. We have to live with it.
(Harris has since published a reply to his critics, which is on my "to-read" list. I'm sure it'll be interesting.)