I noticed that, too - it's a bit of a continuity hiccup, since it has since been firmly established that Logan is thoroughly irreligious - there's a scene where he goes up against Dracula and uses his claws to form a cross, in an effort to drive the vampire back. Dracula swats him away, and says 'that only works if you believe in it'. So having Wolverine talk about prayer seems a bit incongruous. (Of course, one could argue that here was the moment where he LOST his faith, since he prayed to lose his bloodlust for ten years, and lookie here, it didn't work.) Still, it's nice to see Logan depicted as a guy who actually has a conscience about such things, and genuinely tries to contain the animal within, instead of basically saying 'bloodlust? SURE! Slicedyslicedyslice!', as he largely has for a while now.