There are people who are not religious that believe in God, and I'd say God is not necessarily a religious concept. However, to ones who can't or won't discern that difference, they won't have it. Even if they did, they would still call it superstitious and say it is little difference on a venn diagram for they don't want superstition.
However, I can't really find any other grounds to argue on.
I guess the guy was asking to get fired. It's a privately owned business. I agree with Tommy, they're probably covering their hides.
If he had a problem with it, why not find another hardware store that allowed it and in the meantime resign from Home Depot to work there where it was more tolerated? He had plenty of time.