Linda Greenhouse on the Supreme Court and the law.

In the escalating conflict over the new federal requirement that employers include contraception coverage without a co-pay in the insurance plans they make available to their employees, opposition from the Catholic church and its allies is making headway with a powerfully appealing claim: that when conscience and government policy collide, conscience must prevail.

The rhetoric in which this claim is put forward grows more inflammatory by the day. “The Obama administration has just told the Catholics of the United States, ‘To Hell with you!’ ” according to Bishop David A. Zubik of the Diocese of Pittsburgh. The Becket Fund for Religious Liberty, a nondenominational organization that litigates on behalf of religious interests, is circulating a petition under the heading: “The Obama Administration is giving you one year to stop believing” (a reference to the one-year delay the regulation offers to religious employers). Mitt Romney, the likely Republican presidential nominee, joined the chorus this week, calling the regulation “a violation of conscience.”

This aggressive claiming of the moral high ground is close to drowning out the regulation’s supporters, inside and outside of the Obama administration. Maybe I’m missing something, but I haven’t seen a comparably full-throated defense of the regulation, issued last month by the Department of Health and Human Services, except on pure policy grounds. (And there are indications this week that even some in the administration, or at least in President Obama’s campaign apparatus, may be getting cold feet.) While the policy grounds are fully persuasive – the ability to prevent or space pregnancy being an essential part of women’s health care, one that shouldn’t be withheld simply because a woman’s employer is church-affiliated – the purpose of this column is to examine the conscience claim itself, directly, to see whether it holds up.

An obvious starting point is with the 98 percent of sexually active Catholic women who, just like other American women, have exercised their own consciences and availed themselves of birth control at some point during their reproductive lives. So it’s important to be clear that the conscientious objection to the regulation comes from an institution rather than from those whose consciences it purports to represent. (Catholic women actually have a higher rate of abortion than other American women, but I’ll stick to birth control for now.) While most Catholics dissent in the privacy of their bedrooms from the church’s position, some are pushing back in public. The organization Catholics for Choice, whose magazine is pointedly entitled Conscience, is calling on its supporters to “tell our local media that the bishops are out of touch with the lived reality of the Catholic people” and “do not speak for us on this decision.”

But suppose the counter-factual – that only half, or one-quarter, or five percent of Catholic women use birth control. The question would remain: Whose conscience is it? The regulation doesn’t require anyone to use birth control. It exempts any religious employer that primarily hires and serves its own faithful, the same exclusion offered by New York and California from the contraception mandate in state insurance laws. (Of the other states that require such coverage, 15 offer a broader opt-out provision, while eight provide no exemption at all.) Permitting Catholic hospitals to withhold contraception coverage from their 765,000 employees would blow a gaping hole in the regulation. The 629-hospital Catholic health care system is a major and respected health care provider, serving one in every six hospital patients and employing nearly 14 percent of all hospital staff in the country. Of the top 10 revenue-producing hospital systems in 2010, four were Catholic. The San Francisco-based Catholic Healthcare West, the fifth biggest hospital system in the country, had $11 billion in revenue last year and treated 6.2 million patients.

These institutions, as well as Catholic universities – not seminaries, but colleges and universities whose doors are open to all – are full participants in the public square, receiving a steady stream of federal dollars. They assert – indeed, have earned – the right to the same benefits that flow to their secular peers. What they now claim is a right to special treatment: to conscience that trumps law.

But in fact, that is not a principle that our legal system embraces. Just ask Alfred Smith and Galen Black, two members of the Native American Church who were fired from their state jobs in Oregon for using the illegal hallucinogen peyote in a religious ceremony and who were then deemed ineligible for unemployment compensation because they had lost their jobs for “misconduct.” They argued that their First Amendment right to free exercise of religion trumped the state’s unemployment law.

In a 1990 decision, Employment Division v. Smith, the Supreme Court disagreed. Even a sincere religious motivation, in the absence of some special circumstance like proof of government animus, does not merit exemption from a “valid and neutral law of general applicability,” the court held. Justice Antonin Scalia wrote the opinion, which was joined by, among others, the notoriously left wing Chief Justice William H. Rehnquist.

A broad coalition of conservative and progressive religious groups pushed back hard, leading to congressional passage of the tendentiously titled Religious Freedom Restoration Act. It provided that a free exercise claim would prevail unless the government could show a “compelling” reason for holding a religious group to the same legal requirements that applied to everyone else. After a Catholic church in Texas invoked that law in an effort to expand into a landmark zone where no new building was permitted, the Supreme Court declared the Religious Freedom Restoration Act unconstitutional as applied to the states. The law remains in effect as applied to the federal government, although its full dimension remains untested.

Senator Rob Portman, an Ohio Republican, sent a letter to Attorney General Eric Holder on Monday asserting that the contraception regulation violates the Religious Freedom Restoration Act, and it’s not unlikely that one or more lawsuits may soon test that proposition. The question would then be whether the case for the mandate, without the broad exemption the church is demanding, is sufficiently “compelling.” Such a case would pit the well-rehearsed public health arguments (half of all pregnancies in the United States are unintended, and nearly half of those end in abortion – a case for expanded access to birth control if there ever was one ) against religious doctrine.

The court has recently been active on the religion front. In a unanimous decision last month, the justices for the first time recognized a constitutionally-based “ministerial exception” from laws concerning employment discrimination. An employee deemed by a church to be a “minister” – in this case, a kindergarten teacher in a Lutheran school who had received ministerial training and taught some religion classes – cannot sue the church over an adverse employment decision, the court held in Hosanna-Tabor Evangelical Lutheran Church and School v. Equal Employment Opportunity Commission.

The plaintiff, supported by the federal government, had argued that the 1990 Employment Division v. Smith decision precluded the recognition of a ministerial exception from generally applicable employment laws. Rejecting that argument in his opinion for the court, Chief Justice John G. Roberts Jr. explained: “But a church’s selection of its ministers is unlike an individual’s ingestion of peyote. Smith involved government regulation of only outward physical acts. The present case, in contrast, concerns government interference with an internal church decision that affects the faith and mission of the church itself.”

That language is certainly suggestive of deference, beyond the employment area, to a church’s doctrinal claims to special treatment. But while all nine justices signed the opinion, that doesn’t necessarily mean that all nine would agree on its application to the contraception requirement. The question would be whether a church that has failed to persuade its own flock of the rightness of its position could persuade at least five justices.