Carrie,
I probably could have written the exact same thing you just posted. I started HRT about 2 months ago. My wife also didn't want to kiss on the lips or have sex. (Ironically, our sex life has always been more lesbian like with very little PIV sex.) She didn't want to have any expectations and disappoint. Eventually after a few weeks she started to kiss me on the lips again. When she finally realized I was going through with this that's when things started going crazy. Even though she has attractions towards women, (she's never had sex with a woman, but has kissed and received sexual stimulation from a woman through BDSM, we are a kinky couple as well in the BDSM scene) she says that she isn't attracted to me as female, at least not yet. There are times when she does, but she gets in denial about it. (More about that below)
Anyway, later she would get mad and say that I kissed her on the lips blaming me for initiating the kiss. From that point on I pointed it out when she kissed me on the lips and she started to realize that she was initiating kissing on the lips. Then one morning, 3 weeks after starting HRT, she initiated sex and and we were both very happy for a few days. She never blamed me for crossing any boundaries when this happened. A week later she started with not wanting to have sex again. (Signs of denial because even though she is bisexual, she has never been out with her parents who live in TN and although not religious, are conservative.)
Things started getting better again and then we decided it was time to tell her parents I was transgender. (All of my immediate family and our close friends already knew.) So we told them together over the phone and at first they seem to take it well. However the next day her father started talking to my wife about how I was forcing her to become a lesbian and was mad at me. He even sent me an email saying that I shouldn't force her to stay as the person we knew by (<my male name>) would not do this. I responded politely and set things straight (no pun intended) that I wasn't forcing her to do anything and that I love her so much, that I would rather see her leave me to be happy than to stay with me and be miserable. That did keep him from continuing with his logic and he even apologized to me. However, every time my wife talks to her parents, she gets upset because they feel she needs to be "rescued". This is getting better now over time and I'm a little upset that my wife hasn't fully come out to them as bisexual or of having an experience with a woman before and liked it. She has only hinted by saying that she has found women attractive in the past. Of course I'm not going to out her, but I feel she needs to correct this.
Anywho, back to your wife. I would say, that many of her issues have to do with outside influences. One thing is for sure, if society wasn't so ignorant and was more open minded about things, it would make transitioning so much easier. Most of the problems in our relationship dealing with transitioning are problems created by outside influences such as my wife's parents and some of her friends.
This morning we were talking about her friends. Some of her friends think that my wife should be angry for me transitioning. My wife is not angry about it and understands why I'm transitioning. She is hurt by it, and realizes that it's something I need to do for myself, but she is not mad at me. Now she is starting to realize that she is better off not listening to some of these people and tell them she is fine and to leave it alone. Fortunately she does have many friends who understand both sides of the equation and those are the ones you want to keep and talk to. Once your wife starts to realize these things, I think that will help. It's not easy and it takes a lot of time and patients and there will be arguments. However, as long as everyone is civilized and have constructive conversations with great communication you can get through this and determine the best course of action between you and your wife.
-Sydney