When Sue leaves, she and Jude kiss passionately; reflecting on it, Jude sees it as a sign of his alienation from the ministry, an indication of his being unfit to profess the conventional beliefs. He thinks of the fact that Arabella hindered his aspirations to knowledge and now Sue has interfered with his desire to enter the church. He therefore burns all his theological works, so as not to leave himself in a hypocritical position. Sue berates herself for being weak but when she sees Phillotson again she tells him of Jude's holding her hand, not his kissing her. That night she sleeps apart from her husband and the next day asks if she can live away from him. She tells him that she married him because she could not think of anything else to do and was frightened by the scandal at the training college. She argues that "domestic laws should be made according to temperaments," when Phillotson says her request is irregular. When he asks what she means by living away from him, she says she meant living with Jude, not necessarily as his wife, but in any way she chooses. In a series of notes exchanged between their classrooms as they teach, Phillotson agrees only to letting her live apart from him in the house.
When one night Phillotson mistakenly enters Sue's room, she leaps out of the window and slightly injures herself, later explaining to her husband that her action was caused by a dream, an explanation he doesn't believe. Phillotson goes to see his teacher friend Gillingham, in a nearby town, to have someone to talk to. Admitting that Jude and Sue "seem to be one person split in two," he tells his friend that he has decided to let Sue go, her jumping out the window being the final sign of her unwillingness to stay with him. Against Gillingham's arguments, Phillotson can only say that his instinct tells him to set Sue free, though it is opposed to all he believes in. He tells Sue of his decision, and on the day she is to leave they discuss only practical matters. After Sue leaves, Gillingham comes to call.
Hardy is quite right: the kiss Jude and Sue exchange before she leaves Marygreen is a turning point for him. Very quickly, Jude is shown deciding he must give up a career in the church, and he burns his theological works in the garden of his aunt's house. Returning to Phillotson, Sue sleeps apart from him, asks to live away from him, and very soon is allowed to leave him to go to Jude.
It is a turning point in those relationships which embody the structure of the novel. Jude is giving up any hope for a career: "he was as unfit, obviously, by nature, as he had been by social position, to fill the part of a propounder of accredited dogma." And even if he says that he will no longer profess anything although he may believe as before, it is obvious he is reaching the point where he doubts too much to believe as he did. Sue's instruction plus what she means to him has reached a ready pupil. Since he is willing to give up so much for her, to let his emotional life take precedence over his dream of a career, he is ready for her to come to him.
Though Sue believes as she has from the start, perhaps because she does, she is ready to give up a marriage that she has never believed in. That she is ready for a different relationship than that she has had with Jude before is another matter, but giving up on Phillotson, in a sense she has no one but Jude. The radical change in her beliefs comes later.
An interesting aspect of Hardy's narrative method here is the way he shows the deteriorating relationship between Sue and Phillotson. Sue debates with her husband, almost formally, with references to authorities. Their discussion finally collapses into a series of notes exchanged between their classrooms. Their communication is really no communication at all, and it becomes ludicrous.