So a Christian bookstore, for example, that lets employees wear buttons with various Christian messages, must allow employees to wear buttons that say, "Up with atheism", or "Nietsche was right"? You're probably right that a court would enforce exactly that, but it's a sad, sad loss of freedom in our country. If I want to start a company and, being my private property, hire only people that agree with my religious and political views, that should be my right.
The law says you can't. Don't like it. Change the laws or don't open a business.