This "Baptist Press" (BP) article identifies some areas where such questions might be seriously pondered.
Then, while you are still pondering whether same-sex marriage laws might be worth serious thought in terms of their consequences related to other religious freedoms, ponder the other article I have chosen to feature.
In a Frisco, Texas, public school, Gideons applied to place Bibles in a display area where other non-school related items are permitted to be placed, items such as boy scout literature, summer camp program information, and other literature which might be of interest to school children and their parents. The BP article noted:
"The district has what it calls a "viewpoint neutral" policy on such material, provided it meets strict guidelines for decency and civility."
The Gideon's request was approved based on the school district's specific criteria for approval or denial of such material.
What is interesting, to me, is that both articles deal with religious freedom but, from slightly different angles. One group seeks to create state or federal law, forcing a secular (or gay) agenda to be respected in the spiritual institution, the other group seeks permission to make religious material available (not distributed by mandate), under an existing and already implemented policy of a public institution.
The first article linked is fairly exhaustive in citing instances where special "rights" granted to same-sex couples could effect religious freedoms in many ways. There is no mention of any special "rights" being sought on the part of spiritual institutions which would effect secular freedoms or other religious institutions' freedoms. Perhaps there are no spiritual institutions seeking any special "rights?"
In the second article linked, we find that some parents are protesting the simple placement of Bibles next to other non-school related literature in a public school. Those parents, who protest, claim there is no place for the Bible in public school. There is no mention that these same parents had any objection to any other non-school related material being allowed in the display area. Perhaps there are no parents who object to other non-school related material being allowed in the display area?
The secular (or gay) "rights" seekers have little legal precedent for limiting the religious freedom of those within spiritual institutions, beyond the IRS' federal taxing authority requirements on those institutions, which limit their endorsement of specific candidates for office by a promised loss of tax-exempt status should they do so.
The Frisco Independent School District has a valid, legal argument for their policy decision:
"Those opposing the recent distribution of the Bibles must understand that if the District prohibits the Bibles from being placed in the distribution area, it must also prohibit all groups such as those identified above, from utilizing the distribution area as well. The law requires the District to permit all or none, there is no middle ground."
There seems to be little tolerance of religious freedom in America today. Ironically, while intolerance seems to be growing against religious freedom in America, the religious are the ones regularly accused of intolerance.
Are all people in the United States treated equally?