The point is that government should infringe religious practice and belief as little as possible, and only for a very good reason. Aspects of shariah law would be intolerable, although even there, if a burkha was mandated for women, one could choose not to work there. Here, the government is forcing owners of a private company to pay for actions that go against their beliefs, a ridiculous and unnecessary law in any event since birth control costs practically nothing and is hardly being “denied” by the employer.
Many companies require employees wear their clothes a certain way or wear uniforms so a burka would be just another uniform.