When it comes to gay marriage a business owner may not support a homosexual couple wanting to get married, not because they are homosexual, but because they do not believe in same-sex marriage and may even consider it an act of evil that would contradict their conscience.

So the difference is in the first case it would be discrimination against a person. In the second case it is not discrimination against a person but the withholding of participation in a perceived evil.

To see that this is not discrimination against a person or homosexuals let's consider the possibility of two heterosexual males wanting to marry each other (seems highly unlikely but a logical possibility). However, the business owner refuses to help because he is against same-sex marriage. One could hardly accuse the business owner of discrimination against homosexuals since they are not homosexual. (Why two heterosexual males would want to marry each other is strange but not the issue. Perhaps they are being paid. Or they want to claim certain tax benefits). The issue is about same-sex marriage, not the persons sexual orientation. The business owner is not discriminating against anyone here. He refuses to help marry any same sex couple, whether they are homosexual or heterosexual. Ultimately, because he refuses to participate in evil.

To give a further analogy to illustrate my point. Imagine Hitler asking a business owner to supply him with gas ovens for the purpose of killing jews. If the business owner refused it wouldn't be an act of discrimination against Germans fuhrers but rather the business owner's refusal to comply with evil based on his conscience. Should society treat this as an act of discrimination against Hitler or should they appeal to reason and see it as an act of conscience, the refusal to participate in evil?