Underneath the Deacon's pose of why-can't-we-all-just-get-along meekness lies an ideologue just as uncompromising as any atheist. And good for him: It's nice to see him take an actual position. He's wrong, of course, but it's nice to see him at least definite enough to be wrong.
The Deacon makes a few obvious errors in his post. He says without substantiation, "[A]theists believe that... the absence of God releases humans from metaphysical bondage and opens wide the gates of possibility." This is an over-generalization. Atheists—apart from not believing in God—don't all believe anything, any more than Christians all believe anything. It's not even the case that atheists mostly believe that the lack of a God "open[s] the gates of possibility". It is an actual fact that most atheists have very prosaic and respectable ethical beliefs.
The Deacon, in his usual intellectually lazy manner, speaks as if it were obviously the case that everything good comes from God: He does not even bother to grace us with any sort of an argument or substantiation, just a series of bare assertions and assumptions. His argument is technically kind of correct: If there were none of the things that he enumerates, our ethical beliefs would be minimal indeed. He's incorrect, though: Not even the jackboot and the straitjacket would then be entailed, just pure law-of-the-jungle individualism. (Unsurprisingly, we see exactly law-of-the-jungle individualism in non-human animals, more-or-less thinking creatures without much capacity for abstract or self-referential thought.)
But take a look at the things he throws in the middle of his list conflating them with disbelief in God: "no unveiling beauty in creation that reveals ever deeper layers of meaning; no darkly brilliant mystery to existence that defies our mind but illumines our spirit; no moral intuition through which to name the good and condemn evil". These are, of course, things that exist in fact. People do have a sense of beauty we do find layers of meaning. We do apprehend mysteries which excite the mind. (We atheists do tend to want to solve mysteries, and we reject the spiritual benefits of ignorance.) Most importantly, we do have ethical intuition. These are ordinary human feelings. It's typical of the Deacon's arrogance and unjustified self-righteousness that he truly believes that someone who doesn't make a fetish of ignorance and superstition can have actual human feelings or believe them to be important.
The Deacon makes both a scientific and a philosophical mistake as well (he's packing a lot of error into a short post). Philosophically, he's deriving an "ought" from an objective (not a mind or a property of a mind) "is": If the physical universe is not fundamentally ethical, then we ought not to have ethical beliefs. This position was adequately rebutted by Hume. The scientific mistake is, of course, that we're "governed by chance." Even speaking rhetorically, this is a howler: We are, of course, governed by physics, which has no small few non-chance-like components.
Most rational people—including the Deacon himself—reject scriptural literalism (of any scripture) as a complete axiomatic ethical foundation. It is only the scripturalists (whether that scripture is the Bible, the Koran, or the works of Marx, Rand or even Kant) who are in "metaphysical bondage". The Deacon adequately proves in other comments that this task is at least partially possible to theists; Communists and Randians prove that even atheism by itself is not sufficient to release one from metaphysical bondage. It is not disbelief in God that releases humans from this bondage, it is disbelief in the fundamental ethical authority and veracity of scripture—any scripture.
Lacking the authority of scripture, talk about ethics must cast about for a new epistemic authority for this talk to be about something. And that epistemic authority is, of course, ethical intuition. (Keep in mind the difference between authority and veracity; authority entails only that the whole statement ("I believe that 'torturing babies is wrong'") is true by definition; veracity entails that the content of the statement ("I believe that 'torturing babies is wrong'") is true.)
If ethical intuition is our epistemic authority, then any ethical belief system must therefore account for our ethical intuitions; It is irrational to adopt any ethical belief which contradicts the authority of our ethical intuition. If your ethical system entails that you do not believe that 'torturing babies is wrong' and you actually believe that, then your ethical system is false-to-fact and irrational. Secondly, Occam's razor entails that the veracity—in some sense—of our ethical intuitions is the simplest hypothesis, and should be abandoned only if accepting the prima facie veracity entails a contradiction or over-elaboration.
There are a lot of different ways of discussing what it means for an ethical intuition to have "veracity", but these ways are side issues. Just looking at ethical intuition as an epistemic foundation shows the fallacy of the Deacon's argument. For his argument depends on contradicting moral intuition. There's nothing false-to-fact about jackboot and the straitjacket; the Deacon is not making a physically evidentiary argument. He's trading on the actual fact that the jackboot and the straitjacket offend our ethical intuition. But if ethical intuition is any sort of epistemic basis, then the fact that some ethical system would severely contradict our intuition is itself a sufficient argument against that ethical system.
I think the Deacon has a fundamentally misguided view about atheism and naturalism. This post reveals the Deacon's own metaphysical bias of ontological priority: We make certain presuppositions about how the world is, and then reason from those presuppositions to what we know and what we approve of. But that's simply not the case. Metaphysical naturalism has a bias of epistemic priority. We make presuppositions about what we know directly, and then construct a view of the world which explains that direct knowledge. We know perceptual experiences as experiences directly; the physical sciences are a set of ontological theories which account for those perceptual experiences. We know our ethical intuitions as intuitions directly; naturalistic ethics are a set of theories which account for those intuitions.
Update: (20 May 07) The Deacon has deleted the contents of his blog; the post I criticize here is no longer available.
 The short version of the argument is that ethical choices, in the way that humans uncontroversially talk about ethics, always choose between physically possible alternatives. Both alternatives of an ethical choice reference—in a loose sense—that which is. Therefore, we cannot derive an ought from an is in this sense.