"...What's the problem with that?..."
The Chik-fil-A situation is very interesting. If you were to put up a sign that said “Help wanted, particularly Christians” you would be in some mighty deep stuff with the EEOC and nine yards of aggrieved parties. But, simply have a policy of being closed on Sundays and you have no problem. From my experience dining in Chik-fil-A restaurants over the past 22 years, the employees are a real cut above. They draw from a much better talent pool than the average fast food joint.
So, the lesson is, while you cannot discriminate in the employment process on the basis of [a very long list of characteristics, including religion] you can accomplish proxy discrimination by changing the game. Resulting in much better employees and much more satisfied customers.