The Christian Science Monitor has a thoughtful article on whether the proposed Freedom of Choice Act would negate conscience clauses that protect hospitals and doctors from having to do abortions. Ben Arnoldy writes:

Some say FOCA is so broad it would also imperil "conscience clauses" that protect hospitals and doctors who refuse to perform abortions because of their convictions. That's led some Catholic leaders to threaten to close their hospitals if FOCA forced them to provide abortions.Rhetoric aside, it's not certain that FOCA will move in Congress, much less get passed in its current form. Scholars are divided on whether the current bill actually jeopardizes conscience clauses though they agree it is too vague.

That's not to minimize the issue at all - the Monitor does it justice by giving it detailed treatment and pointing out how unclear the bill is on this point. ACLU, take note. It's a civil liberties issue.