I believe the order forces those who own/operate/manage private pharmacies and chains to sell Birth control as well. That's the argument. To counter your statement, Why does there need to be a law, if the employee refuses the owner can fire them.
What I had in mind was a pharmacist in a store's employ who refused to dispense birth control even though the store carried it. If the Pharmacist is in business for himself there in no law that compels him to carry birth control unless I severely misread this article. Aren't they claiming to have a right to to sell something even if they work for someone else?