The game lets us see there's just too much history between these two for me to care enough to be honest with Yennefer. I believe the dialogue choices I'm given at that point don't accurately represent how I feel. Is there any other way to resolve this? If I choose to tell her I still love her, will I be able to tell her the truth later on, and then give her the right reasons for my choice?
No, if you want to be free from Yennefer, you have to tell her that with the removal of the wish your attitude to her has changed, that you don't love her. If you tell her that you still love her, the game locks you on her.
CDPR made this Last Wish the variable, whether you are with Yennefer or not. From a lorewise viewpoint it is questionable, but it is how it is.
I also thought that we will have more dialogues with both woman.