For the past several months, the US Conference of Catholic Bishops has been waging war on the Obama administration over reproductive health care, declaring it no less than a battle over religious freedom. But on Friday, a federal judge ruled against the bishops in a fight over whether the group could impose its views on contraception and abortion through its control of taxpayer dollars.

For the past six months, the bishops have complained very publicly that the administration is anti-Catholic and biased against religious groups because it refused to renew a contract with the group to provide services to victims of human trafficking. The bishops had been administering virtually all the federal money allocated for such services, about $3 million a year, doling it out to subcontractors who served victims all over the country. The USCCB had prohibited the contractors from using the federal funds to pay for staff time to counsel victims on contraception or abortion, or to refer them for such services. (Federal money can’t be used to pay for abortions except in the most extreme instances, but it can pay for contraception.)

In 2009, the ACLU sued HHS, arguing that such rules violated constitutional prohibitions on mixing church and […]