This has nothing to do with 501(c)(3) exemptions.
The Obamacare mandate applies to every employer in the USA who offers insurance to their employees, and every insurance provider in the USA.
Obama wants to frame this as "Catholic bishops vs contraceptive-using Catholic women." Gotta admit it's a brilliant tactic of misdirection.
What it really is, is (1) the Government's successful push to tell every person in America what kind of insurance coverage they can and cannot get to care for their very own bodies, because "all YR health care R belong to us"; and
(2)the Government's rapidly developing power to tell every church in America what kind of beliefs it will be permitted to preach and to live by, and
(3) the absolute supremacy of the State over every individual and every institution in civil society.
#1 necessarily and swiftly entails #2 and #3, but you couldn't tell that to the geniuses at the USCCB 2 or 3 years ago.
Now they're shaking the cobwebs out of their heads and muttering, "Whoa. Something about 'subsidiarity'..."
But it's a little late.
The sacrament of abortion shall not be blasphemed.