President Barack Obama (Pic by The White House, via Flickr)

This past Friday, a judge ruled in favor of the Obama administration in a legal challenge filed by the United States Conference of Catholic Bishops over the religious group’s loss of federal funding.

Late last year, the Bishops lost millions of federal dollars for their relief program for victims of human trafficking. They lost the funds because they refused to refer victims for contraceptives or abortion. Three other groups were awarded the grants instead. Following the loss, the group filed legal action.

Mother Jones reports today, however, that the Obama administration did not “impose its views on contraception and abortion through its control of taxpayer dollars,” which is what the Bishops were alleging in their complaint.

According to Jones:

On Friday, a federal judge in Massachusetts essentially validated the Obama administration’s position, ruling in favor of the ACLU in the lawsuit over the contract. Even though the bishops no longer have the contract, they had joined with the ACLU in asking the judge to rule in the case to settle the constitutional issues. US District Judge Richard Stearns explained why the bishops were in the wrong. He wrote:

To insist that the government respect the separation of church and state is not to discriminate against religion; indeed, it promotes a respect for religion by refusing to single out any creed for official favor at the expense of all others….This case is about the limits of the government’s ability to delegate to a religious institution the right to use taxpayer money to impose its beliefs on others (who may or may not share them).

Stearns also cited an earlier Supreme Court ruling that found that the Framers “did not set up a system of government in which important, discretionary governmental powers would be delegated to or shared with religious institutions.” The judge’s ruling is potentially a big one: It calls into question the entire basis of the federal faith-based contracting initiative, implemented by George W. Bush, which gave tremendous power to groups like USCCB over taxpayer dollars. Stearns found, in fact, that it was USCCB that was making the decisions about how the federal anti-trafficking law should be administered—a job that properly rests with the government, not the church.

For years, Catholic groups have asked to be exempt from federal mandates that non-religious groups have to follow, particularly when it comes to birth control and abortion services. They are only asked to follow mandates when they receive taxpayer funding. Throughout most of this time, powerful groups such as the Conference of Bishops have won their fights for exclusion — but lately, the feds are reconsidering some programs.

The bishops have become well known for using their political power to roll back important protections and legal rights, mostly in the realm of reproductive rights. The Bishops have been described as a “group of men with no real background in law or medicine, but blessed with a strong personal interest in women’s bodies [who] have quietly influenced all of the major anti-abortion legislation over the past several years. “

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