Erin,
The first week after I came out to my wife of nearly 12 years...and this was only like six weeks ago...was terrible. The worst heartbreak for both of us that we have ever experienced. I actually had a different profile on here, and deleted it. I wanted to erase any memory of me being trans. I just wanted the marriage to go back to some semblance of a solid foundation.
My wife moved out of the house soon after, and in the process we both realized our relationship as it existed was over. We will never be the husband and wife we were, nor will we ever have again the magic of the relationship that existed. We have history, and that is all.
That said, she moved back in a couple of weeks ago, and to be honest, it has been more special than it probably has been in the 2 or 3 years previous. I think part of it is that we are "dating" and trying to redefine the marriage. Part of it is that neither of us want it to end. Like your SO, she has told me she is not a lesbian. She also said there will come a point in the transition where she will decide to leave, though she does not know yet what that point is, just as I am not certain how far my transition will be.
For now, we are taking it one day at a time, and I am trying to be very respectful of the pace at which I hit her with new information. We almost had our first week without tears last week, but last night was rough as a good friend of mine shared with us that he is struggling with accepting me (it gave her second thoughts, and led her down the road to thinking about divorce).
The pain you have is very raw right now, but it will get better. It will also get better for her. You should seek a professional counselor, though, if you have the means. They will help with perspective, and also give you a safe place to vent.
Good luck,
Toni