She was his excuse to act out and publicize his ideals, although I don't doubt that he was in love with her.
However, there is much that points to the fact that he was getting tired of her towards the end.
He especially resented that Yoko kept blocking his relationship with his first son, Julian. She lost her daughter, I don't remember if she died or if the child was given custody to her father, and she refused to let John have a relationship with his son.
She did more harm to him than anything else. But, John let himself fall into that situation because he had mother issues, so he's not without blame himself.