The controversy over the Catholic Church and health care goes beyond birth control.

When the Obama administration decided that birth control coverage would be mandatory for all insurance policies, even those provided to employees by large religious institutions, the outcry from Catholic leaders and social conservatives surprised a lot of people. But conflicts between health care and religion, particularly Catholicism, are not news in many parts of the country. Just ask physicians in Sierra Vista, Arizona.

Sierra Vista is a rural community about 80 miles southeast of Tucson and about 20 miles north of the Mexican border. It has one hospital: the Sierra Vista Regional Health Center. In 2010, administrators announced that their secular institution would be joining the Carondelet Health Network, a system of Catholic hospitals. The intention was to make the hospital more financially viable, the administrators explained, but it would also entail some changes: The obstetrics service would have to abide by care directives from the Catholic Church. Although the merger would not be official for another year, staff would begin observing Catholic medical guidelines right away.

The hospital did not perform elective abortions, which is typical for small conservative communities. But the obstetricians were accustomed to terminating pregnancies in the event of medical emergencies. And just such a case presented itself one November morning, when a woman, 15 weeks pregnant, arrived at the emergency room in the middle of a miscarriage. According to a deposition later obtained by The Washington Post, the woman had been carrying twins and passed the first fetus at home in the bathtub. When she arrived via ambulance, she was stable and not bleeding. But the umbilical cord from the first fetus was coming out of her vagina, while the second fetus was still in her uterus.

Robert Holder, the physician on duty who gave the deposition, said the odds of saving the second fetus were miniscule. Doctors would need to tie off the umbilical cord and put the woman at severe risk of infection. After discussing the options, the family, with some difficulty, opted for a medical termination. But, under the new rules, Holder had to get approval from a nurse manager and eventually a more senior administrator. When Holder briefed the administrator, she asked whether the fetus had a heartbeat. It did, he said. “She replied that I had to send the patient out for treatment,” Holder later recalled. He arranged for the woman to get the procedure at the nearest major medical institution—in Tucson. According to his account, the 90-minute trip put her at risk of hemorrhaging and infection, which did not happen, and “significant emotional distress,” which did.

Holder said that an official from Ascension Health, which oversees Carondelet, told him earlier that the rules permit terminating a pregnancy when a spontaneous abortion seems inevitable. (Officials from Ascension and Sierra Vista were not available for comment.) But Bruce Silva, another obstetrician on staff and an early skeptic of the merger, told me that confusion over the rules was common. “We couldn’t get a straight answer,” Silva says. “There was so much gray area. And sometimes you need to make these decisions quickly, for medical reasons.” Even when the new rules were clear, Silva adds, they sometimes prevented physicians from following their best clinical judgments, not to mention their patients’ wishes. A prohibition on tubal ligations, a surgical form of sterilization that severs or blocks the fallopian tubes, meant women had to go elsewhere for this procedure. However, physicians routinely perform this operation as part of a cesarean section, either when patients have requested the procedure or when it’s medically recommended, in order to avoid a second invasive surgery and the attendant medical risks. “I had a patient who was blind. She and her husband were working but poor, and she was diabetic, too,” Silva told me. “She was having her second baby, and that’s all she wanted and she’s got these medical issues. She asked for a tubal ligation. And I can’t do it.”