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The stress due to rape is not chronic stress.

But the stress due to rape is acute stress, isn't it?

Read it again:

"In humans, chronic stress can lead to a drop in sex drive as well as a drop in fertility. [...] Kirby showed that acutely stressed rats showed increased RFRP levels for several hours, but that levels returned to normal by the next day. Chronically stressed rats, however, were left with longer-term elevations of RFRP levels in the dorsomedial hypothalamus area of the brain, and suppression of activity in the reproductive axis - the hypothalamus-pituitary-gonadal hormone cascade"

"It's very adaptive to not be wasting resources on reproduction during times of acute stress, to just shut down reproduction for 24 hours or so until the stress is gone," said co-author Daniela Kaufer, a UC Berkeley assistant professor of integrative biology who looks at how stress affects molecular processes in the brain."

Once again, not understanding the article, also there is no proof that rape would prevent pregnancy from occurring, as many doctors are now reiterating. "Physicians and rape experts say there’s no way the trauma of rape would prevent pregnancy from occurring. “If a woman’s ovaries have already released an egg, she’s just as likely to get pregnant from a rape as she would be from a voluntary encounter,” Dr. Barbara Levy, vice president for health policy at the American College of Obstetricians and Gynecologists. . “From the biological standpoint, a woman is at risk for pregnancy if she’s at a vulnerable point in her menstrual cycle when the rape occurs.”" "Gail Abarbanel, founder and director of the Rape Treatment Center at the Santa Monica-UCLA Medical Center, was appalled by Akin’s remarks. “I think his statement shows such a profound lack of knowledge about rape, the law, and the biology of women’s bodies,” Abarbanel said. “One of the most devastating consequences of rape is getting pregnant. To make the victim responsible for it is outrageous and offensive.” Dr. Amy Rosenman, an assistant clinical professor at the UCLA. “It’s unbelievable. Stuff like that is from the dark ages...there is no physiologic method that prevents pregnancy in the case of rape. If there is an egg available and there are sperm available and they meet, then pregnancy occurs. The ovary and the ovum cannot differentiate sperm from friend or foe.” In fact, each year 32,000 pregnancies result from rape, according to an article published in 1996 in the American Journal of Obstetrics and Gynecology.

The thing you’re missing is the assumption that a woman is ALREADY OVULATING. Stress can wreak havoc on a woman’s fertility, why some women suffer delayed period’s for example, but if a woman is ovulating, and she is raped, once the rapist ejaculates, if sperm meets egg, you’ve got pregnancy, regardless of the “stress” involved.

Kirby showed that acutely stressed rats showed increased RFRP levels for several hours, but that levels returned to normal by the next day. [...] "It's very adaptive to not be wasting resources on reproduction during times of acute stress, to just shut down reproduction for 24 hours or so until the stress is gone," said co-author Daniela Kaufer

The victim may already have ovulated - or may ovulate later and still have in her body the rapist's sperm, which can live for several days. Scant protection there.