For the first time, a federal court has permitted a Health and Human Services (HHS) mandate challenge by a religious nonprofit organization to go forward.

A federal district court rejected the federal government’s motion to dismiss the Archdiocese of New York’s challenge to the HHS anti-conscience mandate.

The U.S. District Court for the Eastern District of New York found that the government’s temporary enforcement suspension against some religious employers, which the Administration misleadingly labels a “safe harbor,” was insufficient to protect the archdiocese and two of its affiliated health care nonprofits from the threat of immediate harm.

The conscience-crushing mandate requires nearly all employers to provide health insurance coverage for abortion-inducing drugs, sterilization, and contraception to their employees, regardless of the employers’ religious or moral objections.

In response to widespread protest over the mandate’s religious freedom problems, the President held a White House press conference in February during which he outlined hypothetical policy changes that would supposedly assuage objectors’ concerns. One affected party referred to the possible changes as a “shell game” that would make insurance companies functionally responsible for the mandated services, complicating bookkeeping without relieving religious institutions’ moral responsibility.

The mandate was finalized without change on February 15, 2012.

At the time it finalized the rule, the Administration announced a temporary “safe harbor,” merely delaying enforcement on some groups until August 1, 2013. The move gave non-exempt religious nonprofit organizations one additional year to figure out how to violate their consciences and comply with the mandate.

The Administration then issued a non-binding “advanced notice of proposed rulemaking” (ANPRM), asking for comments on the “bookkeeping gimmicks” the President offered during the February press conference.

If all of this sounds confusing, it’s because it is. The Administration has argued that it will fix the religious freedom problems before the temporary safe harbor expires, pointing to the ANPRM as evidence. Ten months later, no concrete action has been taken. From a policy perspective, the only plausible conclusion is that accommodating religious objectors is at odds with centralizing health care policy.

Yet the Administration’s argument has caused some judges to treat nonprofit religious objectors’ cases as premature. Until last week.

In the archdiocese’s case, Judge Brian M. Cogan called the enforcement deadline “looming and certain,” like “a speeding train that is coming towards plaintiffs.” As religious liberty advocates have pointed out for months, the non-binding ANPRM “is not a change in policy; it merely seeks input to allow the Departments to consider possible revisions to the [HHS] mandate,” Judge Cogan held. Therefore, it does nothing to shield the archdiocese from enforcement actions against it.

The court observed that the Administration has had plenty of time to address the religious liberty concerns created by the HHS mandate but failed to do so. Ultimately, the court declined to allow the ambiguity created by the Administration’s non-binding promise of some future accommodation to derail the archdiocese’s religious liberty concerns:

[T]he First Amendment does not require citizens to accept assurances from the government that, if the government later determines it has made a misstep, it will take ameliorative action. There is no, “Trust us, changes are coming” clause in the Constitution. To the contrary, the Bill of Rights itself, and the First Amendment in particular, reflect a degree of skepticism towards governmental self-restraint and self-correction.

The archdiocese expects to incur penalties of up to $200 million per year starting January 1, 2014, for failing to comply with the mandate; its health care affiliates face likely fines of $40 million and $400 million, respectively. It has already expended considerable sums in assessing and preparing for its obligations under the new centralized health care regime.

As a result of the court’s decision, the archdiocese’s religious freedom challenge to the conscience-crushing mandate will continue. But religious institutions and individuals should not have to go to court to protect their religious liberty, which the Administration’s policies treat as fundamentally at odds with the core nature of Obamacare’s centralizing, standardizing trajectory.