Indeed, one of his criteria for a sound hypothesis was that it must leave no room for the supernatural. As he wrote to Lyell in 1859, "I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent."
"any one stage" of descent 1) refers to the theory of fossil descent and 2) does not eliminate God from the universe, only from the "equation" by which we calculate descent. Your generalizations are contradicted by the man himself, and an unwarranted over-generalization, in any case.
As the letter I posted shows quite clearly, Darwin was a liar and a hypocrite about his religious views.