I'm in a similar situation now. My boyfriend and I are both cat lovers, but one of his is NOT accepting mine. She's terrified and doesn't seem to be getting over it after weeks of trying...and is not the kind of cat who could adjust well to a new home. So my cat is probably going to have to go to my parents.
Luckily, this will only break my heart, and not hers, because she adapts well to change. I adore that cat and I'll miss her every single day if I have to give her up. But my future with a wonderful man has to come first.