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J. Scott Applewhite, Associated Press
In this Nov. 6, 2013, file photo, Health and Human Services Secretary Kathleen Sebelius testifies on Capitol Hill in Washington on the difficulties plaguing the implementation of the Affordable Care Act.

In politics, timing should never be underestimated.

The White House is insisting that Health and Human Services Secretary Kathleen Sebelius resigned of her own choosing because the enrollment period for the Affordable Care Act was concluded and the program is running smoothly. Politically, however, an earlier resignation would have signaled to the world that the new health-care law was a disastrous failure.

The administration has done all it can to make the case that the 7.5 million enrollments so far through healthcare.gov signal its success. Even though many tough questions about that claim remain unanswered, it provided enough of an window for a graceful exit for Sebelius.

A later exit might have come too close to this year’s mid-term elections, and might also coincide with what some experts predict will be a dramatic increase in health insurance premiums as a result of the law.

But as Sebelius exits after five tumultuous years, she leaves a legacy of troubling questions. Not the least of these involves religious freedom, a bedrock American principle that the Affordable Care Act has attacked from the start. Cabinet members often are charged with carrying out policy directives from the White House, so it is difficult to know how much of this attack is directly attributable to Sebelius, but clearly she was energetic in pursuing the policies.

These attacks involve the law’s contraceptive mandate, which originally would have forced religious organizations to provide such coverage for their employees. After strong objections from the Catholic Church, among others, the administration issued new rules seeking to provide such coverage without making religious institutions directly responsible, a solution that, to believers, served only to highlight how tone deaf the administration seems to the fundamental right to practice religion in all aspects of life.

In the most recent example of this, now before the U.S. Supreme Court, the administration is insisting the mandate must apply to the owners of private businesses, such as Hobby Lobby, nullifying their religious freedom in regard to the contraceptive mandate, which includes coverage for drugs that would terminate pregnancies in the early stages.

It should go without saying that this entire controversy was unnecessary. There is no compelling state interest in mandating coverage for contraception, which is a relatively inexpensive matter that could be left to private choice. The law provides for free contraceptives, but allows insurance to make other important medications subject to co-pays by patients.

These troubling aspects of the Affordable Care Act do not go away with Sebelius’ departure, but they do serve to define her tenure. Her nominated successor, Sylvia Mathews Burwell, faces an enormous challenge as the administration’s promises associated with the act collide with reality, religious freedoms and politics.