WASHINGTON & SANTA FE, NM (By Michael Gerson, WP) November 14, 2011  — In 2009, the University of Notre Dame set off months of intra-Catholic controversy by inviting a champion of abortion rights to deliver the school’s commencement address.

When the day arrived, President Obama skillfully deflated the tension. He extended a “presumption of good faith” to his pro-life opponents. Then he promised Catholics that their pro-life convictions would be respected by his administration. “Let’s honor the conscience of those who disagree with abortion,” he said, “and draft a sensible conscience clause, and make sure that all of our health-care policies are grounded not only in sound science but also in clear ethics, as well as respect for the equality of women.”

Catholics, eager for reassurance from a leader whom 54 percent of them had supported, were duly reassured.

But Obama’s statement had the awkward subordinate clauses of a contentious speech-writing process. Qualifications and code words produced a pledge that pledged little.

Now the conscience protections of Catholics are under assault, particularly by the Department of Health and Human Services (HHS).

And Obama’s Catholic strategy is in shambles.

Shortly before Obama spoke at Notre Dame, the American Civil Liberties Union of Massachusetts brought suit against HHS, seeking to eliminate a grant to Catholic programs that aid victims of human trafficking.

Because Catholic programs don’t refer for abortions, the ACLU alleged that public support amounts to the establishment of religion.

The Obama Justice Department defended the grant in court.

But last month, HHS abruptly ended the funding. It did not matter that an independent review board had rated the bishops’ program more effective than those of its competitors — or that career HHS employees objected to the politicized handling of the grant. HHS announced it was giving preference to grantees that offer “the full range of legally permissible gynecological and obstetric care.”

This was described by one official as “standard procedure.” So it is now standard procedure in the Obama administration to deny funding to some Catholic programs based solely on their pro-life beliefs.

The process that produced the HHS decision remains murky. The USCCB has filed a Freedom of Information Act request for more details. But it is difficult to imagine that HHS Secretary Kathleen Sebelius was not involved in a matter of this much obvious controversy. Sebelius — an outspoken pro-choice Catholic — has a long history of conflict with Catholic authorities.

Broadly applied, the HHS policy would amount to systemic anti-Catholic bias in government programs. And the provocation is one in a series. HHS has drawn conscience protections so narrowly that Catholic colleges, universities and hospitals — any Catholic institution that employs and serves non-Catholics — will be required to offer health coverage that includes contraception and drugs that cause abortion. In global health grants, new language is appearing that requires the integration of family planning and “reproductive health” services, effectively barring the participation of Catholic institutions.

Archbishop Timothy Dolan, president of the USCCB, calls these policies an “assault which now appears to grow at an ever-accelerating pace in ways that most of us could never have imagined.”

The main victims of this assault are not bishops but the poor and vulnerable. USCCB-sponsored human trafficking programs, for example, provide employment assistance, legal services, child care and medical screening.

But because case managers won’t refer for abortions, HHS would rather see these programs shut down in favor of less effective alternatives. This form of anti-religious extremism counts casualties.

It is also politically incomprehensible. Obama’s Catholic outreach is being revealed as a transparent ploy a year before he faces reelection. A portion of the Democratic coalition — including civil libertarians and pro-choice activists — has decided to attack and marginalize Catholic leaders and institutions. And HHS is actively siding against Catholic organizations.

“We are in a war,” Sebelius told a recent pro-choice meeting. Opponents of the administration, she said, are trying to “roll back the last 50 years in progress women have made in comprehensive health care in America.” This is no longer the “presumption of good faith.” It has all the hallmarks of a vendetta.

How will the White House respond?

More specifically, how will the Catholic chief of staff and America’s first Catholic vice president respond?

They gave up their own adherence to Catholic teaching on abortion long ago.

But are they really prepared to betray their co-religionists who still hold these beliefs?

Sebelius is becoming a political embarrassment at an inconvenient time.

It will be significantly harder for Obama to repeat his appeal to Catholic voters while a part of his administration is at war with Catholic leaders and Catholic belief.