Essentially, he’s saying that the incidence of intercourse at the fringes of the fertile period causes conception of far more embryos that can’t survive, and therefore that many more embryos are conceived and then die by this very calculated means than by other forms of contraception. Interestingly, he reports that Roman Catholics have statistically higher rates of miscarriage, at least according to one study — but of course, this is hard to verify.
Still, it seems clear that the rhythm method is at least comparable to the morning after pill or the birth control pill in that it is a manipulation of biochemistry to prevent pregnancy. While the former create an environment that is hostile to embryonic life, the rhythm method instead relies on periods of time during which the female body is naturally hostile to embryonic life. Issues of the effects of the pill aside, it seems to me that if all life, even to the first union of egg and sperm, is absolutely sacred, then some questions must remain in terms of the superiority of this method compared to other forms of reproductive control.