Chani watched you become everything you swore you wouldn't. She fell in love with you because you were a good man who didn't care for power. However, it was now clear that you don't love her enough to give up your power for her.

So, when you decided to fight House Harkonnen and House Corrino in an attempt to end House Harkonnen, and take the Imperial throne from House Corrino, Chani agreed to your plans, but not out of her love for you.

"I won’t be fighting for you. I’ll be fighting for my people." It was obvious that fighting alongside you has nothing to do with you anymore. She's fighting for the same reason she always fought, the safety of her people.