This is so hard!! My wife and I are going through a very similar situation. I told her that I was transgender well before we were married, but we stayed together and she helped me try to "deal with it." Her intentions were never bad. We both thought that I could cope with some middle ground.
Almost exactly two years ago, we had a daughter. Two months ago, I realized that I couldn't live in the middle ground. I had to begin my MTF transition. In the last few weeks, we've had a lot of tears and a lot of unanswered questions of each other. What happens now? She doesn't even consider herself bisexual, much less a lesbian.
My only advice, if one could call it that, is to be patient, take time, and make the decision together. We spent about two weeks coming around to our conclusion-- we were going to tell everyone how I felt. Our friends, our family, my co-workers. Everyone we cared about. That opened up a world of people for her to talk to, to share her concerns with, and to support us both. Going forward, we're just going to take things slowly. I'm growing my hair out.. that will take time. I'm starting HRT. That will also take time.
It's a little harder for me, I think, than just throwing my hands into the air and saying "I've had it-- I'm going to live life as a woman, now." Instead of just taking the plunge, I'm forced to do things slowly, when it already feels like years of frustration pushing me on. But in other ways, the gradual change helps us both to adapt. It helps our friends and family, too. That may not be the best solution for everyone, but it's working for us, so far. There may be a time when she just can't take it, anymore, but she said she's willing to try to make it work until it gets to that point. We're just being open, honest, and communicating constantly.