First, that essay is aimed primarily at those who think dualism is required in order to talk about morality at all - obviously that's not the discussion we are having.
Second, the issue is not whether there are (1) universal (2) morally relevant (3) human preferences that (4) have been created by evolution. The answer to that question is yes (i.e. hunger, sexual desire). But that alone does not show that there is a universal way for humans to resolve moral dilemma.
If we study and quantify the godshatter to the point that we can precisely describe "human nature," we aren't guaranteed in advance to know that appeals to human nature will resolve every moral dilemma. If reference to human nature doesn't, then evolutionary preference doesn't prove moral realism.
I'm not sure why "universality" is really that important here. Suppose we are just talking about one person, why can't they reduce their value judgments down to their own precisely described nature to resolve every moral dilemma they face? With a read-out of their actual terminal values defined by the godshatter, they can employ the usual consequentialist expected utility calculus to solve any question, in principle.
Do you believe in an objective morality capable of being scientifically investigated (a la Sam Harris *or others*), or are you a moral nihilist/relativist? There seems to be some division on this point. I would have thought Less Wrong to be well in the former camp.
Edit: There seems to be some confusion - when I say "an objective morality capable of being scientifically investigated (a la Sam Harris *or others*)" - I do NOT mean something like a "one true, universal, metaphysical morality for all mind-designs" like the Socratic/Platonic Form of Good or any such nonsense. I just mean something in reality that's mind-independent - in the sense that it is hard-wired, e.g. by evolution, and thus independent/prior to any later knowledge or cognitive content - and thus can be investigated scientifically. It is a definite "is" from which we can make true "ought" statements relative to that "is". See drethelin's comment and my analysis of Clippy.