Heh... that's still easy to dispute.There are better ways to phrase the essence of what he's saying that don't cause the argument to rest on premises that are easy to dispute. The writer is correct in that the "problem of evil" (or the existence of things that cause humans to suffer, experience pain, emotional distress, etc.) does not evaporate because one abandons a theistic religion that proposes a one-god will redeem humanity. A better way to frame it might have looked something like this:
Granting that suffering is part of human life, and that this suffering is undesirable, what justifies perpetuating human life when such perpetuation gives rise to more suffering? And, of particular relevance to the religious perspective the author is coming from, how can it be justified when there is no means of redemption? From the author's perspective, addition of further humans only compounds the problem of suffering because there is no "get out of jail" card in the ideologies of what he is describing as naturalism.
Your argument seems to rely on the idea that any suffering at all makes life not worth living. The way I see it, life is worthwhile as long as life is better (and "better" isn't necessarily defined only in terms of lack of suffering) than not being alive... and as far as I can tell, it is better for the vast majority of people.
Also, even if your argument worked and it really was irrational to value life, so what? I don't know any atheists who argue that people are perfectly rational. In fact, I know plenty who argue the opposite.