George Eliot (a.k.a. Mary Ann Evans) grew up in a Christian home but lost most of her religious faith as the years went by. Her novels reveal her agnostic humanism. Let's look at a few examples to get you started.
You might examine the novel Romola, which focuses on a morality apart from religion. Romola's husband is unfaithful, yet Romola cares for her husband's other wife and children, not out of any religious obligation but with some moral sense. The novel also explores the fate of Savonarola in Florence and focuses on Romola's shaken faith.
In Silas Marner, the title character loses his trust in God, and the salvation he finds in the end seems to have little to do with religious faith. He has created a life for himself that does not involve organized religion, and the novel shows the narrowness of some organized religions and their beliefs.
In The Mill on the Floss, you should pay close attention to Maggie. She has a spiritual awakening at one point, after reading The Imitation of Christ, but it does not last, and she turns to worldly pursuits instead, trying to find happiness there. Her devotion is depicted as dull and dry, while what she chooses next is shown as leading to greater satisfaction.
Finally, note the agnostic elements of Middlemarch. You should reflect on Fred's disdain for becoming a clergyman and Mary's condition that she will not marry him if he does. Dorothea has something of a spiritual life, but it is not well formed. She knows little of real spirituality. Mr. Bulstrode tends toward hypocrisy in some ways.