To put it bluntly, wickedness does not characterize the educational experiences of the characters in this novel. Jude, Phillotson, and Sue each have different relationships to education as a pursuit and as a profession.
Jude aspires to be a scholar. He is a dreamer and his dream is to learn Greek and Latin, to study at university, and to become a true scholar. He even hopes to become a bishop for a time, a measure of his ambition. Opportunity is denied him due to several circumstances, the most important being his social station.
Jude is told by the university officials that someone of his class would be better off without a degree.
Rising to the heights of scholarship is too much to hope for, as it turns out.
Phillotson harbors similar dreams:
He nurtures his own dreams of social and intellectual advancement.
Like Jude, Phillotson also abandons those dreams as they prove to be impractical. The romantic ambition for scholarship is unfulfilled for both men as they are denied this particular dream.
Ambition of all sorts leads generally to disappointment for Jude and those he knows. If there is any wickedness to be found in the educational system presented in this novel, we might find it in the brutal treatment of the dreams of those who are honestly drawn to the institutions of knowledge and turned away.
Sue, however, is a talented teacher for a time. The most purely intellectual character in the novel, she is also the one who puts the least stock in ambition, in scholarship, and in the idea of social climbing.
Sue's example suggests that the wickedness of the day related more to social conformity, closed-mindedness, and conventional thinking. It is this kind of conventional thinking that forces Sue and Jude to leave town and later to marry. This pressure to conform is the clearest wickedness in the novel.