Perhaps the most contentious and difficult political-moral-legal issue over the past half-century has been abortion. Many Americans consider it tantamount to murder, whereas others insist that access to the procedure is a fundamental constitutional right. Some activists believe that the state or private employers should be able to force medical providers to perform abortions even if they have sincere religious beliefs against doing so. The advent of emergency contraceptives/abortifacients such as Plan B and Ella raise similar issues with respect to pharmacists filling prescriptions.
In 1973, shortly after Roe v. Wade was decided, Congress passed the Church Amendment to protect health care professionals. The legislation prohibits any court or public official from using the receipt of federal aid to require a person or institution to perform an abortion or sterilization contrary to their “religious beliefs or moral convictions.” The amendment also makes it illegal for health care organizations to discriminate against individuals who refuse to perform these procedures. In arguing in favor of these protections, Senator Frank Church (D–ID) remarked that:

[N]othing is more fundamental to our national birthright than freedom of religion. Religious belief must remain above the reach of secular authority. It is the duty of Congress to fashion the law in such a manner that no Federal funding of hospitals, medical research, or medical care may be conditioned upon the violation of religious precepts.”]
Subsequent Congresses expanded these protections. For instance, in 1996, Congress passed the Danforth Amendment which, according to Robin Fretwell Wilson, prohibits:

the federal, state, and local governments from discriminating against healthcare entities that refuse to (1) undergo abortion training, (2) provide such training, (3) perform abortions, or (4) provide referrals for training or abortions. Specifically, it protected doctors, medical students, and health training programs from being denied federal financial assistance, certifications, or licenses they would otherwise receive but for their refusal.”]
While not limited to institutions that oppose these practices for religious reasons, there is little doubt that an important motivation behind this act was protecting religious actors.
Like Congress, numerous states protect health care providers who have objections to performing certain procedures. According to the National Abortion Rights Action League (NARAL), “47 states and the District of Columbia [have] passed laws that permit certain medical personnel, health facilities, and/or institutions to refuse to provide abortion care.”
It is noteworthy that many (but not all) states specify that their conscience clauses protect individuals who object to abortions on “moral or religious grounds.” Some of these statutes offer better protection for religious liberty than others, but overall, both the national and state governments have made significant efforts to protect the ability of health care professionals to act (or not act) according to their religious convictions in these policy areas.
Recently, heated debates have arisen about various types of emergency contraception (EC).  Some activists claim they merely prevent conception, whereas others contend that they can cause abortions. Some health care providers who believe that ECs can cause abortions and thus end innocent human lives have refused to administer or fill prescriptions for these drugs.
With respect to pharmacies, some states permit individual pharmacists to refuse to fill these prescriptions as long as another pharmacist is available to do so. Others permit pharmacies themselves to refuse to carry such drugs (particularly relevant for small, family-owned pharmacies). Currently, between 16 and 22 states protect health care providers and/or pharmacists from having to provide ECs.
A closely related issue concerns state and federal requirements that employers pay for various types of contraception, including ECs. Some employers have refused to provide health plans covering such drugs. States have moved to protect the consciences of such individuals and entities in different ways. According to NARAL, of the 28 states that require health insurance to cover controversial forms of contraception, 20 exempt employers from doing so if they have religious or moral convictions against these drugs.
At the national level, acting under the authority of the Patient Protection and Affordable Care Act of 2010 (the Affordable Care Act), the Department of Health and Human Services mandated that businesses cover a range of contraceptive devices, including ECs. Religious denominations and houses of worship were exempted from these requirements, but other religious organizations were not.
In response to significant outcry, the Obama Administration issued regulations whereby insurance providers used by religious organizations would offer these drugs at no cost (in theory) to the religious organizations’ employees. Some religious organizations were satisfied by this approach, but others believed they were still complicit in wrongdoing. For-profit businesses received no such protection, but in 2014, the Supreme Court held in Burwell v. Hobby Lobby Stores, Inc., that the Religious Freedom Restoration Act requires such an accommodation for a closely held for-profit corporation.
There is no denying that protecting religious actors who are licensed by the state to provide medical services is one of the most complicated policy areas in which religious citizens have been accommodated. In some instances, such as with ECs, even the basic effect of the drug is debated. Even when it is not, the state’s interest in regulating the provision of medical care, which can involve issues of life and death, is undoubtedly high.
These cases are further complicated because they raise equal protection issues and sometimes concern what the Supreme Court has called a fundamental right to abortion. It is telling that in spite of these complications, the nation and many states have gone to great lengths to protect the moral and religious convictions of health care providers.
Time and experience may reveal that some of the accommodations mentioned in this section are harmful. Although some advocacy groups fear that these accommodations will lead to great harm, there has been little evidence that this is the case. If substantial evidence arises that some of the policies mentioned in this section are detrimental to the well-being of patients, legislatures may have to rethink existing accommodations. If such evidence does not surface, however, legislatures in states without accommodations should move quickly to protect the religious liberty of all citizens more effectively.