After all his statement was about the right to marry, which is a secular legal issue. Even if the state were to recognize same-sex marriages, churches, mosques or synagogues or other places of worship would not be required to hold wedding ceremonies within them or sanction such marriages because the no legal standing is attributed to such ceremonies or sanctions.

That may be so in the US (in the UK most churches and some other religious centres do act as legal instruments of the state when they marry people) but even if it is true, I don't think that covers it sufficiently.

Even if there is no legal service conferred by a church's marriage ceremony, a service is nevertheless offered - the use of the church building, the services of an officiant, and perhaps a musician. Usually this service is paid for. The florist provides the flowers. The limo hire people provide the transport. The photographer provides his or her photographic services. The catering company provides the food. The church provides a venue and a speaker. These commercial services are pretty much equivalent.

If you're saying that a church should be allowed to discriminate in its service provision against people because they're gay (or, by extension, black, Mexican, disabled, female...) then you're implicitly saying that a shop or business should be able to discriminate thusly too. In Britain we have the 2007 Provision of Goods and Services Regulations which make that illegal. I don't know if there is equivalent legislation in the US, but even if there isn't, the principle is still sound. It is morally wrong and should be illegal to discriminate unfairly in the proviison of goods and services. And there is no reason why churches should be exempt from this. Being run by conscientious homophobes is not a good reason. If they offer to marry anyone then they must be compelled to marry everyone who asks.

It is my firm conviction that this fight will not be over until the churches, mosques, synagogues and other religious institutions are compelled to provide their services fairly and to all without discrimination. They do not have the liberty to murder who they want, steal what they want, rape who they want or set what they want on fire. Those "religious liberties" are denied to them, and for good reason. The "liberty" to discriminate is similarly unacceptable in a modern, civilized and morally upright society.