Whether any religion chooses to recognize LGBTQ rights is their business. Religion is in its essence a voluntary enterprise. Usually, one becomes a member because they choose to. As such, if you don't like how things are done, you don't have to remain a member of the institution***.
So, if a church doesn't wish to conduct marriages between same-sex couples, so be it. Same if they do want to allow it. If a same-sex couple wants to be married, but a given church doesn't want to conduct their marriage, the couple can take their business elsewhere.
I do think, though, that denying same-sex couples the opportunity to be married -- on a civil, legal, and cultural basis -- is unethical on principle. Marriages between any consenting persons ought to be permissible and available. Whether one wants to add a spiritual layer to the marital process is up to them, though a religious institution that does allow such unions is ethically preferable to one that doesn't, even though I would not seek to strip these institutions of their right to deny such unions (though I will shake my head at it).
***Of course, things like indoctrination and social pressures and obligations -- as well as the fear of social consequences and stigma due to leaving religion -- will influence why a person will want to remain a member, even if they harbour a desire to leave. Unless one is being coerced into staying, though, it remains that one is free to leave, even if it does incur these consequences and stigmas.