President Obama is changing a controversial rule requiring religiously affiliated organizations to provide birth control to employees by putting the onus on insurance companies to pay for the contraception.
In other words, he is making no substantive change to the policy at all.
Yes and no. Functionally what the policy does is to shift the administration of the plan (at least the contraceptive part) to a secular third party — the insurance company. This gets a bit problematic with respect to self-insured hospitals, say. But it terms of respecting religious scruples of the administration of a college or hospital, a third party shift does look like an appropriate accommodation.
Of course, the deeper desire not to offer contraception even at arms length is not dealt with, but then at lest at state level, case law allows for neutral public policy to over ride religious scruples; faith is not a trump card.