Emma was not a conventional Christian. She was a Unitarian. We were discussing this in church last Sunday. Unitarianism in the nineteenth century was not as liberal as today, but it still stressed tolerance, reason and personal faith rather than literal reliance on scriptural texts. Emma was troubled by her husband's lack of faith, but perhaps less troubled and more supportive than a conventional Christian might have been.
https://web.archive.org/web/20090225124103/http://www.darwinproject.ac.uk/content/view/130/125/
My reason tells me that honest & conscientious doubts cannot be a sin, but I feel it would be a painful void between us. I thank you from my heart for your openness with me & I should dread the feeling that you were concealing your opinions from the fear of giving me pain … my own dear Charley we now do belong to each other & I cannot help being open with you.