They say the use of the Church has to be within guidelines acceptable to their denomination.
And they have a lot of latitude in that regard. If the local Catholic Church in my neighborhood has a Sausage Fest as a fund-raiser for its schools, and I come with a "Bong Hits 4 Jesus" banner to display (or perhaps even a T-shirt with that slogan) they are within their rights to ban my attendance. However, if they have thrown this event open to the public, they're probably not going to be allowed to refuse me entrance merely for being a non-Catholic, even if I've been outspoken on the subject, but within my free speech rights.
Does a church organization have the right to refuse use of its facilities to homosexual people for civil unions, on the grounds that "we don't recognize civil unions", when civil unions (that the Court has mandated have the same legal status as marriages) are all that are available to same sex couples? We're about to find that out.