But ultimately, it still uncertain what will happen with the Little Sisters' health plans, said DeGirolami, because the sisters are self-insured. Self-insured plans are not covered in the court's opinion, he said, "so it's extremely unclear what will happen to them."
However, the court did suggest something significant in the nuns' favor – that their free exercise of religion may have been substantially burdened, Alvare said.
Under the Religious Freedom Restoration Act, the 1993 federal law at the heart of the case, "Government shall not substantially burden a person's exercise of religion" unless the government proves both that it has a "compelling interest" for acting and that it is using the "least restricting means" of furthering that interest.
The court's decision may have confirmed the first part of the law, that the mandate is a "substantial burden," Alvare said. "I'm hard-pressed to think that they [the court] would have allowed this case to go back, unless there were at least strong disagreement there between the justices, or even maybe a majority in favor of the idea that the Little Sisters get to decide if they're burdened," she added.
However, a key concern in the court's decision was that it gave the government a "pass" in having to prove its contraception mandate was in the "compelling government interest," part of the Religious Freedom Restoration Act, she said.
By pushing for a solution where women employees were still guaranteed their contraception coverage, it seems the court "swallowed the [government's] argument that contraception is preventive health care," she explained.
This would be bad reasoning because cost-free contraception for everyone is not a public health necessity, she argued, in part because unintended pregnancy rates have risen despite the government claiming that contraception will solve that problem.
"The very groups that the government has targeted for free or low-cost contraception since the '70s, their rates of abortion and unintended pregnancy have soared," she noted. "People do more risky behavior when they think it's insured against."
Also, in its arguments the government "didn't ever even mention the annual billions of dollars of settlements from contraceptive manufacturers to women who have been injured or have died," she said, a huge liability to their defense of birth control as public health.
For instance, by July of 2013, Bayer Pharmaceuticals had settled claims related to its birth control drugs from over 6,700 plaintiffs totaling $1.4 billion, according to the Chicago Tribune.
"And the idea that this could be a compelling health interest alongside these billion dollar settlements is ridiculous," Alvare said.
(Story continues below)
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The vast majority – "89 percent of sexually-active women" – are "using contraception" already, she argued, and the other women not using it have good reasons which do not involve cost.
"You can make it free, you can hand it out on the street corners. You're probably not going to get more women using it than use it now."
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