The "God" stuff makes up about 90 second of Japanese dialogue, if that. It's one of the character's reactions to their predicament, not the thrust of the film. If anything I'd say the movie's dual goals are to a)make you feel incredibly uncomfortable, and b)put together a truly unpleasant character study of Dr. Heiter. For me, it succeeds at both. Six directs it like FUNNY GAMES, very sterile and impersonal, lots of measured camera movements and minimalist set choices. It's unnerving. And as everyone seems to agree upon, Dieter Laser knocked the Heiter roles out of the park.
The film is blackly comic, but I never found it puerile or lowbrow like you're claiming it to be. It's remarkably restrained given some of the bad-taste jokes the premise opens up.