The fact that people are trying to get laws passed to ban certain types of marriage between live human beings is discriminatory, and in effect, limiting freedom. Now, if a church doesn't want to perform the ceremony, that is 100% perfectly fine. I don't think it's right, and I have just as much right to that opinion and that specific church has to theirs.
It doers NOT, however, justify the mistreatment of employees- many of whom disagree with the owner's stance. I don't eat there anymore, because it is very unhealthy, but customer service wasn't the problem- the sense of "I can treat people however I want" that pervades the younger generation of this country is the problem!