I watched that episode, it was pretty funny and even as somebody who really does not like religion I do agree, if you have a problem with them then just go to the several hundred other resteraunts there are bound to be around, this is the equivalent of religious nutters tryign to sue someone for teaching evolution in a school or something.
There's a pretty big problem now with people clearly not understanding what civil rights actually are, or what freedom of speech is for that matter.
I don't think that it is the same as suing for teaching evolution. There is actually a very pronounced movement to start teaching around science. The Koch Bros are potentially making some progress in inflecting the information contained within school textbooks...
http://www.truth-out.org/opinion/item/27965-is-the-koch-brothers-curriculum-coming-to-your-child-s-schoolPersonally, I think that article is poorly written and requires a few more examples and an expansion on the 'personal responsibility' concept as it applies to individual liberty. If anything, I believe that it inherently excludes contextual and systematic exclusion of certain demographics and industries from being included in the narrative...an abstract of that idea would include a discussion on how big of an impact the advertising industry has on the behavior and attention of individuals per demographic (the opportunity cost of attention...unwittingly spent by people unaware of options).
But suing for the teaching of education is part of a bigger push that has spanned decades. Religion in public schools and the acquisition of government funding for such is a very old battleground. Even the "Equal Access Act", intended for after school Bible study, was considered a very long 'victory' in the making...and is ironically co-opted by LGBT rights.
That said, there is no need to care about discounts given to people who pray. But in a world where the religious right can nitpick over everything and have the mass media trumpet the irrelevancy it seems like fair game to have that go not uncontested...even if it perpetuates irrelevancy. Buys time for people examining the real social dichotomies...