As Richard Dawkins noted in The Blind Watchmaker,
An atheist before Darwin could have said, following Hume: "I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one." I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.
In this same vein, it is my opinion that the way in which it could be said that Darwin Killed God is that he moved the end point of a functional epistemology. If one lived their life based on the evidence and the best reasons they had at hand, prior to Darwin one would have been a rational deist and after Darwin, outright atheism became the natural endpoint to living an evidence driven life.
It has always been the case that there have been scientific ethics and scientific endeavors, since the first of the ancient Greeks questioned the notion of whether or not progress was possible. Whether or not people could understand more of the world than they currently understood. If there exists some way of investigating reality. This is the first scientific conflict with religion.
There has always existed specific scientific virtues of curiosity, empiricism, and progress throughout history. Wherever they are suppressed, science is suppressed. Wherever embraced, science is embraced. When Galen challenged early evolutionists whose theory of transmutation was weak, powerless and wrong, he attacked the ideas with empirical evidence, pushed our understanding of the human body, and yet still concluded that the divine was the most logical conclusions. However, he didn't go beyond his evidence. He didn't propose an infinite God because there were noted limitations within men. He went were the evidence lead him, and the evidence lead him to God.
When ever these virtues are challenged, even by great minds, they end scientific inquiry. Wherever they flourish, science flourishes. Aristotle was a proponent of science in one's own mind. The idea that one could rightly divine by thinking about an issue the correct answer. This idea may seem compelling, but it has always been wrong. It was wrong when Aristotle concluded that objects of different masses fall to Earth at different speeds, it was wrong when Galileo dropped different masses off the Tower of Pisa to see if they did, and it was wrong when the masses struck the ground at the same time. Asking whether or not our beliefs are true, and how we can go about seeing if they are, has always been the scientific way of looking at the world. Wanting the most true beliefs and the fewest false beliefs has always been the core of science and the results of scientific virtues.
Isaac Newton was the greatest scientist to ever live (if this is hyperbole, you'll have to drop a few names). But, he was also a Christian. He wasn't Christian because he was blinded by his faith and wrong about what to believe, he was Christian largely because that is what a rational view of the world would lead on to believe in the 1600s. With no explanation of how life or any part of the universe arises by chance or by simple laws, it would have been absurd for Newton to not conclude theism. That is not to say he wasn't a freethinker. He refused to be ordained as was required by a man of his position because he felt that Trinitarianism was idolatry because the first commandment said that "I am the Lord your God, who delivered you out of Egypt, you shall have no other gods before me" and frankly Jesus didn't deliver the Jewish people out of Egypt so worshiping Jesus is worshiping an idol. And in those places where the scientific ethics failed and religious ethics succeeded they rendered Newton sadly moot. In the end of Principia, Newton concluded that the order of the planets and their interactions between each other must be the result of the hand of God keeping them working. It was another hundred years before Laplace properly explained perturbation theory and did the calculation properly without God ('I have no need for that hypothesis' or so he was rumored to have told Napoleon).
Cunningham cited St. Augustine to make the claim that Christians never really took Genesis as literal. However, what Augustine was really angling at is that they never really took science literally and they shouldn't embarrass themselves in the company of those who do. Augustine wasn't saying that it should be taken as figurative, but that rather it didn't need to reveal scientific facts about the world (which Augustine noted God clearly knew) but that we didn't need to know them. We have no need to be curious about the world because all we need is to be saved and all we need to be saved is the Bible. We don't need to test the world or test God, because we just need to be saved. And even if we could progress in our understanding of the world, it simply isn't necessary to be saved. Augustine wasn't saying that we should throw Genesis out the window and ignore it, he was saying that science is stupid and you don't need it to be saved, so God didn't include it in the Bible. This isn't a hard conclusion to reach, Augustine spelled it out:
In short, it must be said that our authors knew the truth about the nature of the skies, but it was not the intention of the Spirit of God, who spoke through them, to teach men anything that would not be of use to them for their salvation.
This is the division that has always existed between science and religion. Why when we look back through the ages we find many rational and scientifically minded people believing in God in times prior to Darwin and after Darwin we find that these examples cease with a surprising abruptness. Why should Thomas Jefferson, who was perhaps our only scientifically literate president, have said, "He (Calvin) was indeed an Atheist, which I can never be". He derided the newer supernaturalist brands of theology as talks of nothing and to be equivalent to saying that there is no God. Why should Jefferson be a theist when any contemporary individual of such a caliber embrace atheism? I contend that the answer is Darwin.
Cunningham is not only wrong on the obvious points, that Genesis was intended to describe the start of the universe within Christian theology and was clearly believed as mostly literal by a vast majority of Christians throughout the ages. Or that ultradarwinists extremists are trying to use Darwin to argue against God by embracing the Selfish Gene and Memes. Cunningham is also wrong on the core points, there is some respect that we could say that Darwin killed God. We can't accept that literally, as there never was a God to be killed. But, it is safe to say that Darwin made not believing in God the reasonable position to embrace, given a careful and full examination of the evidence. It wasn't until after Darwin and largely because of Darwin that a full embrace of scientific ethics lead to atheism. Darwin moved the endpoint of a functional epistemology from theistic conclusions like those (somewhat non-sequitury) drawn by Paley and others to having no need for God. Darwin made God superfluous. And for a God that does nothing, this is worse than a bullet. A difference, that makes no difference, is no difference. A dead God, or living God, or non-existent God doesn't change a jot or tittle of our existence, and Darwin made all three functionally identical when he explained life itself.