Pharamacists complain that they shouldn't be required to participate in procedures they disagree with. Senators declare that opposing the appointment of judges well outside the mainstream to lifetime positions is religious discrimination. They're hardly alone. Police and military services discriminate against pacifists. Jury selection discriminates against death penalty opponents. People working in corporations struggle with conflicts between personal ethics and job responsibilities every day. No one's coming to their defense.
The aim of all the special pleading isn't to prevent discrimination against people following their consciences. It's to create a privileged conscience. It's to say that there is a particular set of beliefs that should be privileged everywhere, and that those who hold those beliefs should be allowed to impose their beliefs on those around them at any time or place.