Try not to worry, most of the people I know who transition stay with their current partner. Especially if you are supportive, I would still have to say that most will stay. Also, Sexual Orientation has NOTHING to do with gender presentation. Sure they COULD switch, but it has nothing to do with hormones or anything else. Most of the FTM I know(from my partners group)l love males and females and identify bisexual, a couple now identify as gay and only one out of like 20 identify as straight. The MTF also appear to be about the same breakdown.
So, I would say the odds are good in your favor. Also, you two have love so that changes the whole dynamic.