I am so sorry for you and the struggle you are going through. It is a terrible burden. I've done just over 300 posts, and I think 250 of those are about my struggles with marriage after coming out in February. My wife just recently filed for divorce. We were married for 12 magical years.
All I can offer is the pain of trying to make the relationship work, seeing your loved one struggle, and then trying to battle your own inner conflict is hell. I wish I could say it gets easier, but it really will be tough for awhile. It may even get worse before it gets better. At least it did for me. I purged, bargained, and tried to man up. It only made me obsess more about who I was inside. I even went to therapy for several months before coming out, and am still in therapy now. If you are transgender, it will never go away. Only you can decide what you can live with, and that includes balancing relationships, jobs, and being authentic and true to yourself. It differs for everyone, but I have never heard anyone say it is easy.
My wife and I have been very civil, and she is still supportive of my transition - whatever that may be. She just does not want to be married to an effeminate male, and no way to a woman. Even with that said, it is still tough. She cries a lot when I talk to her, and I cry occasionally when we are apart. After a couple of months apart, it is getting easier, though. The good days are beginning to outweigh the sad. I am also starting to assimilate my dual lives of male and female to consolidate them into one. That gives me comfort and peace, if not a little frustration.
I guess my point is to go slow, get a good therapist that you can go to (and encourage her to get counselling as well, if it is an option financially), and do what you can to figure out you. There is no timeline that says you have to have everything figured out in 3 months, 6 months, or 12 months. I know it is heartbreaking and I feel it really strong if I think about my own loss too much, but there is life on the other side, and it is a good life as well.