It’s a question I was never going to give a definitive answer to, of course. Some things Doctor Who CAN’T have an answer to. Faith is one of those things. The Doctor is a scientist, after all. He relies on empirical data, on what can be proven by science. Nine times out of ten he succeeds in doing so. Most of the gods he has ever come across turn out to be fakes. Just occasionally there is something he can’t explain. The Beast in Satan’s Pit was one such. When he was asked afterwards what it was, he simply replied ‘We beat it. That’s good enough for me.” And he never said for certain if it WAS the original and authentic devil. Nor did he answer the question Ida asked him earlier, - “What do you believe in.”
Going further back, to the Curse of Fenric, The Doctor was among many people whose lives depended on having a strong and unyielding faith in SOMETHING. The vicar’s faith in God had been shaken by the war, so he failed. The young Russian soldier believed in Communism and he survived. The Doctor believed in his companions and said their names:- “Susan, Barbara, Ian, Vicki….” as a mantra of protection. The evidence strongly suggests that The Doctor believes in himself and his friends and has no need for faith in an unseen god. But it was interesting to put the question. Just who DOES he turn to when he needs comfort and reassurance. That there seems to BE nobody is one of his vulnerabilities.
The flashback to the adventure in which Rose was injured was, of course, simply to fill in the story. The Doctor’s dilemma on its own did not really make a full story. The back story wasn’t really enough of an adventure by itself. The two together worked just fine.
But I’m not at home to any nonsense about blasphemy. The Doctor simply reflected a point of view shared by many people. And if a short story isn’t the place to explore those views, then what is?