I think Darwin has a lot more credibility than Marx or Freud.
Darwin himself was not an atheist by any means.It disturbed him greatly that some branded his theories as "proof" refuting the existence of God.
He saw no contradiction between natural selection and the presence of God.
Darwin's career reminds me of Samuel Butler's later nineteenth-century autobiographical novel, "The Way of All Flesh." Butler's parents were somewhat early Evangelicals who appear to have subscribed to the Rapture, an idea that first appeared among English Evangelicals during the nineteenth century. I've read some of their letters, and they were obsessed with the idea that the end of the world was imminent. Oddly, and familiarly today, they watched events in the Middle East closely, and took various events there as evidence that Armageddon was at hand.
Anyway, when Butler grew older, he rebelled from his parents, and wrote a novel in which the hero rebels from his parents.
Darwin's situation was somewhat similar: a religious father against whom he appears to have rebelled, in good Oedipal fashion, or perhaps Enlightenment fashion. I agree with you that the evidence is not so clear in Darwin's case as in Butler's, although of course Darwin was one of the influences on Butler's revolt. Darwin has been made out to be both a Christian and an enemy of Christianity, and there's enough ambiguity in his life and writings to have allowed biographers to make both cases.
But I don't think we can be confident that he was a believing Christian in the years when he was writing and publishing his theories.