No one is talking about forcing Churches to perform same sex marriages. We're talking about businesses.
As for your distinction between discriminating based on skin color and on sexual orientation, that's just special pleading. Even if your conception of Christian values doesn't discriminate based on skin color, it's easy to imagine a religion that does, and the government would have to provide freedom to ALL religions equally. This requires upholding criteria external to the religions themselves.
Also, no one is talking about forcing Christians to do business with anyone, just about upholding the law or what's ethical. If Christians don't want to provide service to gay people, that's fine. However, their self imposed restriction may cost them something. They may have to forsake the prospect of running a business at all. Notwithstanding, that is an option available to them. Therefore, they are not being forced.
I used to be Catholic, so I'll have to object to the idea that the Catholic Church would support refusing admission to gay students. I believe they would object only to homosexual acts. So let's instead consider a school run by religion X, which considers merely being gay to be evil. I would say if this school's purpose is in large part to educate its students about religion X, then it could be considered part of the Church of X, provided it satisfies all other legal criteria.