It seem pretty clear that the Obama administration is just being punitive and make religious organizations bear the legal costs of going to court. From Fox News:
The Obama administration says faith-based nonprofits should comply with ObamaCare’s birth-control mandate because they have more leeway than the corporations that won a Supreme Court ruling on the issue last year.
Government attorneys made the argument on Thursday to the Circuit Court of Appeals for the District of Columbia Circuit, after pro-life ministry Priests for Life asked the court to reconsider a ruling it made last fall that requires religious nonprofits to object in writing to regulations that require employer health care plans to insure contraceptives . . .