Science that disregards religion completely is what students are being taught. Miller writes it exactly the same way an atheist would.
Which religion should science take into regard when being taught to students? If it takes one into regard it would have to do the same for all, wasting time that could be spent looking into something that has a basis in science. Should they teach about Norse gods, Hindu beliefs, Scientology? You seem to be saying that students aren't getting exposed to religions in science class but I am willing to bet that you only want one religion to be taught there. Religions are personal, they have no place in the classroom beyond history class.
Not teaching about religion is not the same as teaching that there is no religion. Would you want other personal beliefs such as UFOs, Bigfoot, or ghosts to be taught as science?