The management ideology of both chains are different and have different values. Obviously Chick-fil-A management care about their image and so they have clean stores and superbly courteous employees (at least at the ones around here) where as McDonald's does not. I would venture to guess that Chick-fil-A does pay more and also asks for more in return where McDonald's just doesn't care; cheap food, cheap service, low expectations from customers.
I was thinking about this issue the other day. I was at Chick Fil A for lunch and the difference is night and day as far as the customer service compared to McDonalds/Wendys/Burger King. The restaurants are just plain cleaner and friendlier. I'm not 100% on this, but I think Chick Fil A also pays employees more. The point though is that until McDonalds changes their image and focus, I don't see any reason these employees should be paid more. Will a higher wage mean higher quality service is the real question.