The author finds that the change of allele frequencies over time leads to atheism? Or maybe the author is just doing the Usual Creationist Thing of accusing everyone who doesn't share his viewpoint of being atheists. Oh well, at least he didn't accuse evolution for being responsible for the disappearance of Jimmy Hoffa.
I suspect that a practical application of the moral principles inherent in the idea of "survival of the fittest" may have played a significant role in his disappearance.
I think the author is suggesting that one cannot interpret reality in only a mechanistic, materialist way and pretend that that doesn't affect theology and morality. He concludes that for a Christian it must lead to either atheism or a deformed theology; for the non-sectarian person, it will lead to atheism. It seems a reasonable argument to me.