As I recall, Darwin's sister was the only person present when he died and it's her word that he actually denounced his thoughts...even if he had, it was probably because he was trying to repent because the fear of even the slim possibilty of hell existing would lead him to eternal suffering. But, denouncing all of that would leave him in a position to have a better chance at reaching paradise, and if he didn't...well, so what? He would be dead, and the path of the world would not matter to him in the slightest because he'd cease to exist. Simply put, he was a fearful man --- which is most likely, though this is obviously speculation ---, his sister lied, or he truly did not believe in what he had spent decades working on.