I don't think you've understood what the article is about. At least, you don't really grapple with what I said. The point is that atheism, as in the intellectual rejection of theistic belief is consistent with a behavioural form of religiosity. Thus, atheists aren't necessarily godless in the wider sense.
Regarding your strawmen and red herrings, then, if the atheist gives a pragmatic defense of her faith in reason, the theist could do the same: religious faith would be useful in maintaining social order. So that's a trap for the atheist. Indeed, I've made that pragmatic case for theism in "A Flaw in Dillahunty's Atheism."
Sure, atheists can have a concept of value. The question is whether their choice of values is rational or self-evidently justified, as Sam Harris maintains. If not, atheists may select their values, goals, and ideals in a quasi-religious way, in which case they're not fully godless.
Regarding atheism and skepticism, you're talking as if atheism were a philosophy. Atheism is only the rejection of theistic beliefs. The question is about the atheist's positive worldview, be it neoliberalism, pessimism, communism, naturalism, or whatever. My point was just that a godless worldview would be highly skeptical of all myths, mass delusions, and faith-based conceits.
Where on earth does the article commit the genetic fallacy or make this "argument from origins"? Honestly, I reread it and I can't tell what you're talking about. Indeed, my recent article, "Nietzsche and the Creativity of Losers" shows how Nietzsche commits that fallacy.
If you're going to level these charges, don't you think you should be quoting from the article to show you're not just slinging mud for no good reason, like a crazed chimp?