So I went looking for laws regarding discrimination, and found that although they protect people from discrimination in employment, they don't seem to give people the right to services or products. If you search for "right to refuse service" you'll find that almost every website with a page of legal fine print has a section outlining their right to refuse service to you, for any reason. I wasn't able to find any federal laws to counter-act this, except in the case of housing. You cannot be refused housing (buying or renting) on the basis of gender, marital status, pregnancy, etc.
Based on my quick analysis, therefore, churches will not be required to provide marriage services to gay couples, if such marriages become legal at the state or federal level(s), if they don't want to. In fact, they can also refuse to marry people based on the color of their skin, creed, or any other factor. By the same token, boy-scouts can refuse memberships to girls, and the KKK can refuse to admit catholics (you did realize that the KKK isn't just anti-black, right?)
Employment is trickier. For the moment, churches (and believe me, the federal laws are very vague on what "church" or "religion" or "belief" mean) are somewhat exempt even from anti-discrimination employment laws. They may refuse to hire, say, a pastor on the basis of creed, gender, etc. The Mormon church considered negros (their own words) to be a "cursed" race, whose children should (and would) never serve in the priesthood. The Southern Baptist Convention was formed when baptists in the south were told that slave holders would not be allowed to be missionaries, as the parent organization at the time was pro-abolition. Women have been (and still are) excluded from certain positions of ministry (you can find the relevant Bible verses yourselves) -- refusing to marry a gay couple certainly isn't out of the ordinary.
Though a church may refuse to marry you for whatever reason, churches do not have a monopoly over marriage. This freedom of theirs to refuse services therefore does not hinder your ability to receive such services from elsewhere (your local government outlet mall, known as the county courthouse.)
Civil Rights Act of 1964, Title II
Okay, so I'm glad absolutely nobody took the time to tell me about this. I went looking again, because I wanted to know why segregation on buses was still not permitted (under the assumption that it isn't, or we might still be seeing it.) Congress did pass several laws specifically targetting public transportation. But the Civil Rights Act of 1964 extended anti-segregation legislation quite a bit. Under Title II, you'll find that, in fact, discrimination on the basis of "race, color, religion, or national origin" is prohibited in places of commerce. It lists hotels, restaurants, movie theaters, and other places of entertainment, as well as any attached businesses. The law does specifically mention "commerce" -- there should be value-based trade involved, from what I can tell. The law also clearly targets state, county, and city laws allowing segregation. Further, Section 201 (e) exempts "private clubs" that are open only to a pre-selected clientele.
Clearly, I was only seeing Titles VII and VI, repectively proscribing segregation in employment and particularly in federally-assisted programs. I should have looked around in that same document.
So, now, having found this, what do we say about churches? I suppose we could say that they are private clubs. Indeed, churches generally refuse to provide services such as baptism or marriage to non-members. Many churches require that you be a member for a full year before such services become available. They may also require letters of recommendation. That, to me, says that it might be considered a private club, and therefore exempt.
Besides, the Civil Rights Act of 1964 doesn't mention "gender" or "sexual orientation" in the list. Does that make you happier?