This is of course an internal question to the religion, any religion. It is not the law of the land to impose values, beliefs, and practices into religion, and absolutely not the other way around either, try as hard as some do to impose religious values on those outside the religion!
As society as a whole becomes more tolerant, more open-minded, more educated and knowledgeable, this will itself gradually bring about change from within the religious institutions they are part of. Change takes a very long time though. It takes key people at the top for it to begin to trickle down, and those key people arise from within the body itself. My favorite saying is that change happens one funeral at a time. I think that sums up a lot of what we see.
I can go into some length about this, but I think it's safe to say the government is not forcing religions to adopt its beliefs and values and practices. And it it my belief that those who are crying about their "rights" being stripped away, such as not being "allowed" to pray in school, taking "God out of the classroom", etc., are deflecting attention off their own personal religious agenda to proselytize others to their beliefs and values by having special status. If they government actually did legislate prayer in school, and that prayer happened to be Muslim prayer, once again they would feel they were being marginalized because it wasn't their religions prayer! It's pretty obvious the game there.
I am all for people having the right to choose their own partners for marriage, and to enjoy the legal status of the land. But I also would agree that if a church structures itself to say only certain people qualify for certain internal privileges, that should be their right to practice their religion as they see fit. If someone doesn't like what they do, go elsewhere, or work from within to change the system.
All that has happened here in laws like these, is to protect those in society who do not share those same beliefs and values of certain religious groups. As well it should be. I would not want to have some freaky fundamentalist group deny me the right to meditate because they ignorantly believe it's "of the devil", or something. Or force me to wear black clothing made of wool and not drive a car. Or say I can't listen to certain types of music, or a long, endless list of things that religious does internally, and sadly feels the need to spread to the world beyond its own doors. That's all that happening, is that right to NOT practice that religion is being enforced.