I don't get the impression that Hitch has much empathy for religious people, and so he does a bad job of understanding what it is they actually believe. It doesn't help that the most vocal members of our community are rarely the smartest or the most disinterested and convincing. (Did he really quote Ann Coulter in this article? I don't even know what to say. I didn't even realize she was a Christian.)
I mean, even in my more fundamentalist youth, I never would have had a problem with the micro-evolution necessary for Salamanders to lose their eyes. And as for the whole idea that there's something perverse about the idea of God designing a species that will eventually lose its sight, well I don't really see why that is perverse in first place, but a much stronger argument would be to ask what kind of perverse God would intelligently design diseases. And that's really just coming back to the problem of evil or the problem of pain. There are religious answers to the problem, which a person may or may not accept, but anyway, none of this has anything to do with Salamanders. The problem of pain has been around ever since humans began contemplating the possibility of a just and all powerful God.