TL;DR: Galilee, where Jesus lived and preached, is a metonym for Christian morality; Cyprus, where Aphrodite emerged from the sea, for pagan sexuality.
Even if the references are obscure, I think it’s possible to figure out the meaning from the context. At the end of book II chapter II of Jude the Obscure, Jude Fawley is struggling between his infatuation with Sue Brideshead, and his Christian morality:
He [Jude] affected to think of her [Sue] quite in a family way, since there were crushing reasons why he should not and could not think of her in any other.
The first reason was that he was married, and it would be wrong. The second was that they were cousins. It was not well for cousins to fall in love even when circumstances seemed to favour the passion. The third: even were he free, in a family like his own where marriage usually meant a tragic sadness, marriage with a blood-relation would duplicate the adverse conditions, and a tragic sadness might be intensified to a tragic horror.
But then at the beginning of chapter III, Jude attends the church of Cardinal College and hears the choir singing Psalm 119:
Wherewithal shall a young man cleanse his way?
And he thinks he sees a way to reconcile his passion for Sue with his Christianity:
The girl for whom he was beginning to nourish an extraordinary tenderness was at this time ensphered by the same harmonies as those which floated into his ears; and the thought was a delight to him. She was probably a frequenter of this place, and, steeped body and soul in church sentiment as she must be by occupation and habit, had, no doubt, much in common with him. To an impressionable and lonely young man the consciousness of having at last found anchorage for his thoughts, which promised to supply both social and spiritual possibilities, was like the dew of Hermon, and he remained throughout the service in a sustaining atmosphere of ecstasy.
(“The dew of Hermon” is a reference to Psalm 133: “Behold, how good and how pleasant for brethren to dwell together in unity! […] as the dew of Hermon, that descended upon the mountains of Zion”.)
We suspect that Jude is fooling himself, and that by ‘social’ he really means ‘sexual’:
Though he was loth to suspect it, some people might have said to him that the atmosphere blew as distinctly from Cyprus as from Galilee.
So even if we don’t recognize the references, the metaphor must be that ‘Galilee’ represents Christian fellowship and morality, and ‘Cyprus’ pagan religion and sexual love. Galilee is the region of Palestine where Jesus lived and carried out his ministry. Cyprus was sacred to Aphrodite, the Greek goddess of love. According to Hesiod’s Theogony, when Kronos castrated his father Ouranos, he threw the severed genitals into the sea, and
a white foam spread around them from the immortal flesh, and in it there grew a maiden. First she drew near holy Cythera, and from there, afterwards, she came to sea-girt Cyprus, and came forth an awful and lovely goddess, and grass grew up about her beneath her shapely feet. Her gods and men call Aphrodite, and the foam-born goddess and rich-crowned Cytherea, because she grew amid the foam, and Cytherea because she reached Cythera, and Cyprogenes because she was born in billowy Cyprus, and Philommedes because she sprang from the members.
(Translation by Hugh Gerard Evelyn-White.)
The reference to Cyprus as the birthplace of Aphrodite is somewhat obscure, but it dovetails with one of the major themes of Jude the Obscure, that is, the contrast between the pagan sensuality of classical religion and the chaste austerity of Christianity. For example, in book I chapter V the young Jude addresses a prayer to the goddess Diana:
On a day when Fawley was getting quite advanced, being now about sixteen, and had been stumbling through the “Carmen Sæculare,” on his way home, he found himself to be passing over the high edge of the plateau by the Brown House. The light had changed, and it was the sense of this which had caused him to look up. The sun was going down, and the full moon was rising simultaneously behind the woods in the opposite quarter. His mind had become so impregnated with the poem that, in a moment of the same impulsive emotion which years before had caused him to kneel on the ladder, he stopped the horse, alighted, and glancing round to see that nobody was in sight, knelt down on the roadside bank with open book. He turned first to the shiny goddess, who seemed to look so softly and critically at his doings, then to the disappearing luminary on the other hand, as he began:
“Phœbe silvarumque potens Diana!”
But then he regrets this and resolves to restrict himself to the study of Christianity:
Reaching home, he mused over his curious superstition, innate or acquired, in doing this, and the strange forgetfulness which had led to such a lapse from common sense and custom in one who wished, next to being a scholar, to be a Christian divine. It had all come of reading heathen works exclusively. The more he thought of it the more convinced he was of his inconsistency. He began to wonder whether he could be reading quite the right books for his object in life. Certainly there seemed little harmony between this pagan literature and the mediæval colleges at Christminster, that ecclesiastical romance in stone.
In book II chapter III, following immediately on the Cyprus/Galilee passage, Sue meets a pedlar selling miniature statuettes of classical deities.
They were in the main reduced copies of ancient marbles, and comprised divinities of a very different character from those the girl was accustomed to see portrayed, among them being a Venus of standard pattern, a Diana, and, of the other sex, Apollo, Bacchus, and Mars.
Venus is, of course, the Roman name for Aphrodite. Sue buys a Venus and an Apollo, but then is embarrassed by her impulse:
When they were paid for, and the man had gone, she began to be concerned as to what she should do with them. They seemed so very large now that they were in her possession, and so very naked. Being of a nervous temperament she trembled at her enterprise. When she handled them the white pipeclay came off on her gloves and jacket. After carrying them along a little way openly an idea came to her, and, pulling some huge burdock leaves, parsley, and other rank growths from the hedge, she wrapped up her burden as well as she could in these, so that what she carried appeared to be an enormous armful of green stuff gathered by a zealous lover of nature.
“Well, anything is better than those everlasting church fallals!” she said. But she was still in a trembling state, and seemed almost to wish she had not bought the figures.
Occasionally peeping inside the leaves to see that Venus’s arm was not broken, she entered with her heathen load into the most Christian city in the country by an obscure street running parallel to the main one, and round a corner to the side door of the establishment to which she was attached.
When her landlady confronts her about the purchases Sue pretends the two statuettes are:
“St. Peter and St.—St. Mary Magdalen.”
and later on, after Sue has unwrapped them:
Occasionally she looked up at the statuettes, which appeared strange and out of place, there happening to be a Calvary print hanging between them, and, as if the scene suggested the action, she at length jumped up and withdrew another book from her box—a volume of verse—and turned to the familiar poem—
Thou hast conquered, O pale Galilean:
The world has grown grey from thy breath!
So again we have a contrast between Venus and Galilee. The poem that Sue reads is Swinburne’s ‘Hymn to Proserpine’ which imagines a pagan believer lamenting the triumph of Christianity.