That sounds pretty rough and I feel for you.
Honestly, you need to do what's right for you. If you suppress your feelings just to be with her you may:
1. Feel resentment towards her.
2. End up even more upset (not being your true self)
Also...there is no guarantee she'll still be with you (regardless of what choice you make) < Not trying to sound negative but it is the truth. Don't hang on to something that is not there.
If you feel it is not working [like literally gone past the point of no return] you may as well both end it amicably. Don't try and work on something that is clearly never going to work....In the same breath maybe you two could sit down and talk about it all? Let her come to terms with it and also for you to understand where she is coming from?
- Never, ever, ever, ever, ever live your life for someone else. Do what makes you happy...if transitioning is where you want to be then get working on it

I wish you all the best - quote me if you need anything.