So you're saying that On the Origin of Species left out God as a creator? Too bad nobody told this to Darwin:
Edit: in On the Origin of Species, Darwin doesn't present evolution as some sort of "God-free" system. To the extent that he mentions God at all, he uses his theory to show God as an all-knowing architect who could set a process in motion and leave it than as an imperfect tinkerer who has to continually adjust his Creation to get it to run properly. In this regard, the theological picture that Darwin presents is a lot like Newton's.
My own impression of Darwin's religious evolution is that he went from being a Bible-believing Christian to becoming something of a more liberal Christian when he was aboard the Beagle. At least his views on creation changed and I get the impression quite grudgingly. He compared admitting that evolution is true to confessing a murder, IIRC, which indicates to me that his theory of "descent with modification" is a hypothesis he came to very reluctantly and wished that the religious views that he started out with were true.
After reading an essay by Stephen Jay Gould titled "Darwin's Sea Change: Or Five Years At the Captain's Table", I came to think that having to put up with the captain of the Beagle really dimmed his view of Christianity, coupled with the horrible thought that his father, grandfather, and other freethinkers in his family would suffer for eternity in hell. When he was conducting his research on the origin of species, I think the quote you mentioned above shows that he embraced a sort of deism. There was a creator who made the universe, designed the laws of the universe, and may have even made the very first life forms, but since then left natural selection to take over for him.
I think he transitioned from being a deist, to being an agnostic, then to being an agnostic nontheist. I think it was the death of his daughter which destroyed a belief in any kind of god, loving or not. Losing his daughter may have been the straw that broke the camel's back for him.