How is Jane Eyre both a deeply religious and a deeply irreligious novel?

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Jane Eyre both attacks the conventional religious hypocrisy of the Victorian era and depicts Jane as a deeply moral, feeling and upright person who is true to her Christian faith as she understands it. 

The novel depicts religious hypocrisy through the figure of Mr. Brocklehurst, surely one the more odious characters in English literature, who lives in warm, well-dressed, well-fed comfort while subjecting the girls at the Lowood School Jane attends to a harsh regime of hunger, cold and mortification of vanity through short hair and plain clothes, a regime meant to improve their souls. Jane experiences intense anger at the deprivations Mr. Brocklehurst forces the girls to endure for their spiritual salvation while apparently not feeling he or his family needs such moral improvement or suffering. Thus, the novel calls into the question conventional religious morality that allows the poor to be treated differently than the rich for "their own good." 

Jane loves the deeply religious Helen Burns, but Jane also rebels at Helen's long suffering patience in enduring hardship, unfair punishment and ultimately death at Lowood. The novel thus calls into question the limits of female submission in the name of Christianity. Jane's own heart burns with a far more rebellious flame than Helen's, one shocking to Victorian audiences in its desire for freedom. Likewise, while the adult Jane admires St. John, she cannot marry him despite his deep religious faith and missionary zeal, because she cannot accept his emotional coldness.

Though the novel rejects the kind of religious conventionality that can damage the human spirit, Jane remains morally upright. For example, she reacts with extreme distress and horror when she realizes that Rochester is trying to trick her into a bigamous marriage and when she finally understands that he has his insane wife hidden in the attic. She believes in the religious sanctity of the marriage bond and runs away rather than compromise her values. Further, although she cannot love everyone, Jane follows her conscience and tries as far as she can to treat all people with Christian love and fairness as well as she can: it is this moral strength of character that attracts Rochester despite her lack of good looks or high spirits.