He meant to give Fred his full advantage, but it would be well, he thought, to clear her mind of any superstitions, such as women sometimes follow when they do a man the wrong of marrying him as an act of atonement.
And I wish to make atonement to you as the one still remaining who has suffered a loss through me.
There are no more uses of "atone" in the book.
Show samples from other sources
To atone for sins is a common religious theme.
Approved forms of faith, practice, and conduct were laid down as consistent with orthodoxy, and deviation from these standards had to be confessed and atoned for by a prescribed form of penance.
Dictionary of the History of Ideas -- http://etext.lib.virginia.edu/cgi-local/DHI/dhi.cgi?id=dv1-50(retrieved 05/20/06)