There is a short list of attributes one cannot legally discriminate for or against in the US - race, sex, religious affiliation, pretty much sum them up. Those attributes are singled out from all others - being a pirate or police officer or guitar player, being a fan of some sports team or musical group, etc - for what we considered good reasons, when we made them special. There is a history here, a set of facts that trump any kind of logical system that would reason, say, that being Catholic is akin to being a Yankees fan, so any bar that offered half price drinks for a game ticket stub and the right cap could likewise offer free booze to anyone who showed up with an Ash Wednesday thumbprint on their forehead. Historically, too much blood has been shed over that ash mark and its related circumstances, and we've had enough.
It sounds silly, but the protestations of innocence around discounting for prayer are not realistic either - as others have pointed out, we all know the discount is in fact for Christian prayer, and in particular Protestant, and joins a power struggle in which the goal is white male Protestant supremacy. The innocence of such a discount depends on a core of good faith that we have good reason to doubt, and so despite the triviality of the thing it is in fact illegal - we have banned that category of business promotion, and for very good reason. We have learned that you can't fool with religion and its affiliations - it's too dangerous.
On the other hand, the automatic devolution of the argument to atheist vulnerability is tangent - surely most of the people who have ever prayed on this planet have been atheistic, in the current sense of Deity. I don't know what the official Wiccan position on Deity is, but Buddhists and Taoists and trad Navajo and animists and so forth all pray, or most of them anyway, and it is generally considered a good thing to do regardless of one's theistic leanings. Atheists don't have to lie to pray - they just have to get their ducks in a row re humility and such.
