On the voyage of the Beagle, he did not doubt the literal truth of the Bible but sought explanations in the laws of nature and saw adaption of species as evidence of design. He remained quite orthodox and would quote the Bible as an authority on morality. Like the rest of us, he questioned the cruelty of nature when seen in the light of an all loving God. One such example was the ichneumon wasp which paralyzed caterpillars as live food for its eggs. Darwin still believed that God was the ultimate lawgiver.
That's what I think anyway,