I've read your question a few times. It does sound like you two have come to an impasse. It sounds like there are several values here -- your own stoicism, following individual conscience/top-down morality, your values and your wife's values on LGBT issues (see, it hurts straight childless people too, it's not just "them").
But I think the only thing I keep thinking that you really need to know right now is this: unconditional love. unconditional love. unconditional love.
Nothing can be as toxic in a personal relationship -- whether it's a romantic once, a parent/child one, or, I'd argue, a relationship with whatever deity one believes in -- as feeling you aren't really loved.
And it does sounds like you love her.
But she's probably not feeling that way right now.
I certainly don't know whether you, the husband, should keep showing up at the pews every day. Robert Kirby does. (Seriously, if nothing else, go read his column on a "part-active marriage." It's fantastic.) But this is your wife, and she's hurting. She's not even hiding the fact that she's hurting -- her hurt and betrayal is out there in an ugly cry every time some jerk says something. Sometimes those jerks are her ecclesiastical leaders. It sounds like more and more, that is indeed the problem: her conscience is telling her that this is not a safe and okay place for her to be.
I don't think you want to be part of that hurt. You're her husband. If you can't be there for her now, and quietly let her cry and sleep in on Sunday and browse Reddit and whatever else she needs, I honestly think that she will in fact feel pushed away from her. My opinion comes from personal experience. I did not ever marry (temple or no), but if I had along the line, that's what I'd want. Knowing that my husband put our marriage first. Because that's what the Gospel says, right, to put your family first?
She likely feels stigmatized and angry already. I hope that building a strong relationship together can help ease your own numbness. You're not in your marriage alone. Please don't cut her off when she needs you most
Differing views on this religion was a large part of why I was estranged from my mother for a good year. When I reconnected, she already had stage IV cancer. I missed out so much, and she's dead, and I really wish we had been able to get through that impasse. I regret it every day. I'm inactive, I have no desire to go back, and I still regret the rift every. single. day.
Ending with a line from the Kirby:
Hope something in there can help you. Good luck to you both.You'll get lots of advice about what to do in your split-faith relationship, nearly all of it from people who have no idea what the hell they're talking about. There's nothing easier to give someone else than advice that doesn't apply to you.
In the end it came down to this for me: I believe the most important thing for which I'll be judged is how I treat my wife rather than my church.