Soon after the enactment of the Patient Protection and Affordable Care Act of 2010 (ACA), or Obamacare, the Department of Health and Human Services (HHS) announced that qualifying health insurance plans under the law would have to cover contraceptives and “morning after” pills. Many religious institutions — most notably the Catholic Church —objected to being forced to fund products and procedures that offend their religious beliefs. This particular mandate may be among the less costly parts of the Affordable Care Act — as we learned from the Sandra Fluke imbroglio, birth control isn’t that expensive — but it certainly struck a nerve and is the subject of much of the “second wave” of Obamacare litigation.

In August 2011, HHS bowed to political pressure and provided exemptions to certain religious organizations, those that only serve people of their own faith and are engaged only in religious activities. That is, the exemption covers churches — presumably only churches that don’t provide social services — but not the panoply of religious institutions, such as schools and hospitals, that aren’t purely worship institutions. And it certainly doesn’t exempt businesses run by religious people, whose objections are identical: being forced by the government to do something against their religion as a condition of continuing in operation.

Accordingly, more than 40 cases challenging the challenging the contraceptive mandate are now active across the country by various individuals, religious institutions, nonprofit organizations and small businesses. District courts have split on the lawsuits, though many have dismissed them as being premature — because final regulation have not yet been promulgated and the mandate only went into effect this past New Year’s Day.

Two of those suits were consolidated late last year for the first appellate argument on the issue: one brought by Wheaton College, a Christian liberal arts college in Illinois, and another brought by Belmont Abbey College, a North Carolina college based around a Benedictine abbey. The legal point here is somewhat technical, but incredibly important for anyone who thinks his freedom of conscience may be violated by the government in the future (a category that includes essentially everyone).

As noted above, the contraception mandate came to include a narrow exemption for religious institutions, one that wasn’t available to religiously affiliated colleges. After the strong backlash against even that “narrowed” mandate, HHS issued a “safe harbor statement,” saying that the government wouldn’t enforce the mandate for a year (until August 2013) against certain nonprofit organizations religiously opposed to covering contraception. In other words, the contraception mandate is still in place but just won’t be enforced — but only for a year and individuals are still free to sue to enforce it against their religiously opposed employers.

HHS also issued an Advance Notice of Proposed Rulemaking (ANPRM) that announced the department’s consideration of more permanent methods of accommodating religious institutions. Because of the safe harbor notice and the ANPRM, the district court dismissed the colleges’ lawsuits for lack of standing and ripeness, holding that the colleges weren’t suffering any injury and it was too early to challenge the proposed rule. The case thus went to the U.S. Court of Appeals for the D.C. Circuit, where the colleges argued at a December 14 hearing that they are in fact suffering a current injury — having to plan for a Hobson’s choice — and that the mere possibility of a future accommodation is too remote to terminate their case.

The Cato Institue filed an amicus brief [PDF] supporting the colleges in that technical argument, joining the Center for Constitutional Jurisprudence and the American Civil Rights Union. We argued that the trial court misapplied the constitutional test for standing by not focusing on the facts that existed at the outset of the case; subsequent government actions, such as the ANPRM, are irrelevant to the preliminary question of standing. We also argued that the district court’s ruling compromises the principle of separation of powers by allowing the executive branch to strip a court of jurisdiction merely by issuing a safe harbor pronouncement and an ANPRM (which doesn’t legally bind an agency to act in any way). It was thus entirely speculative whether the agency would alleviate the harms that the colleges are suffering.

Without intervention from the courts, therefore, the colleges would be left in legal limbo while facing immediate and undeniable harms to their religious freedom: On one hand, they can’t challenge the constitutionality of a final regulation. On the other, they can’t very well rely on a proposed regulatory amendment that may be offered at some unknown point in the future. The trial court rulings in the Wheaton College and Belmont Abbey College cases were thus frightening examples of judicial abdication that permit the expansion of executive power far beyond its constitutional limits.

Fortunately, the circuit court agreed. In a brisk three-page opinion [PDF] released December 18 (four days after argument), the per curiam court held as follows: (1) the colleges have standing because that’s assessed at the time lawsuits are filed (here, before the ANPRM); (2) the government’s representation that the rule would never be enforced in its current form is “binding”; and (3) the government must update the court every 60 days. Accordingly, the lawsuits shouldn’t have been dismissed and are instead to be held “in abeyance” pending “the new rule that the government has promised will be issued soon.”

Assuming that the government doesn’t act in contempt of court, religiously affiliated nonprofits — or service organizations, or whatever the final wording will be — will thus join religious-worship institutions as exempt from the mandate.

But that’s not the end of the matter. Employers engaged in for-profit activity, including those who have the exact same objections as Wheaton and Belmont Abbey, will still be forced to choose between continuing their business and maintaining their religious principles. Most notable among these companies is Oklahoma-based Hobby Lobby, Inc., the art-and-crafts chain that employs 21,000 people and has well over $2 billion in annual revenues.

Hobby Lobby lost its motion for a preliminary injunction against the mandate, the Tenth Circuit declined to issue an injunction pending appeal, and, on December 26 — coincidentally St. Stephen’s Day, honoring Christianity’s first martyr — Justice Sotomayor (as circuit justice) declined to provide such an injunction as well. Thus, when the mandate went into effect last week, Hobby Lobby became potentially subject more than $1 million in daily fines.

That’s a shame. If we’re to respect religious belief, why does the motive of those espousing them matter for whether the government gets to trample them? The owners of Hobby Lobby donate plenty to charity out of the profits they make, possibly having greater impact than many of the nonprofits that are (or will be) exempt. Dven if they didn’t, however, this country was founded on ideals of religious liberty that went on to be enshrined in the First Amendment, so why would we just ignore them?

Indeed, when one of these lawsuits finally reaches the Supreme Court — which it will unless at least this part of Obamacare is repealed — the plaintiffs should win without even getting to the constitutional claims. That’s because the Religious Freedom Restoration Act prohibits the government from placing a “substantial burden” on the exercise of religion unless it has a “compelling interest” and uses the “least restrictive means” to achieve it.

Americans understand that the essence of religious freedom is that government can’t force people to do things that violate their religious beliefs. Some may argue that there’s a conflict here between religious freedom and women’s rights, but that’s a “false choice” — as the president himself like to call such things. If the HHS rule is repealed, women will still be perfectly free to obtain contraceptives, abortions and whatever else isn’t against the law. They just won’t be able to force others to pay for them.

But there’s an even bigger issue here. This is just the latest example of the difficulties in turning health care — or increasing parts of our economy more broadly — over to the government. As my colleague Roger Pilon has written, when health care (or anything) is socialized or treated as a public utility, we’re forced to fight for every “carve-out” of liberty. Those progressive Catholics who supported Obamacare, or the pro-life Democrats who voted for it, who are now appalled by certain HHS rules should have thought of that before they used the government to make us our brother’s keeper.

The more government controls — whether health care, education, or even marriage — the greater the battles over conflicting values. With certain things, such as national defense, basic infrastructure, clean air and water and other “public goods,” we largely agree, at least inside reasonable margins. But we have vast disagreements about social programs, economic regulation and so much else that government now dominates at the expense of individual liberty. Those supporting Wheaton and Belmont Abbey Colleges and Hobby Lobby are rightly concerned that people are being forced to do what their religious beliefs prohibit. But that all comes with the collectivized territory.