But a gay business owner cannot discriminate against the very religious groups who seek to exclude gay people from their institutions or services. Gay people do not even galvanize around such political positions as, say, banning Christian marriage or Christian adoption, or supporting the firing of Christian employees.
It's illegal to refuse service to a Christian on the grounds of his religion but it's not illegal for a painter to refuse to paint a mural if he finds its message (which may be religious) revolting.
Any conclusions drawn by the Court in this case will be readily extrapolable to religious affiliation. Web designers don't have to do a "We're gay and we love it" site because it offends their religious beliefs? Then other web designers don't have to do a "This is our Catholic church" site because Catholicism offends their Protestant beliefs.
(IANAL, but this would, perhaps, be a good argument for the defendants to bring).