Ok, well I strongly expect that many on the right think this is at least one of the major things which it provided protection from.

The first statement of the link provided seems to back up this view:

Remember the Bush Administration's "conscience rule"? The one that would have allowed health providers to deny patients treatment based on religious grounds? The one that would have allowed pharmacists to deny women access to contraceptives simply because they thought contraceptives were immoral?

It doesn't seem to be talking about employees; it appears to be talking about organisations as a whole who choose not to provide certain services.

I think this is very much worthy of clarification.