When we ask if a government should allow a company to use religion as a basis for discrimination, we've reached a level of abstraction that defies any intuitive moral reasoning. Now if one thinks morality exists in an absolute metaphysical sense, then this isn't an issue. The author however is an atheist, and so has no possible moral justification argument that would be convincing to their religious coworkers.
The belief that notions like equality and anti-discrimination would hold any weight in a society of secular thought has now become about as laughable as Communist economics after the fall of the USSR. Now "discrimination" is merely a line used by each tribe in turn to justify why they should be owed special treatment for their victimhood. The weight of each group and individual "getting theirs" will not be bore for long. So I guess the author should enjoy his "ice cream" while he can. After all, it's not like (he thinks) there's any one to judge him for it anyway.