Miss Bates stood in the very worst predicament in the world for having much of the public favour; and she had no intellectual superiority to make atonement to herself, or frighten those who might hate her into outward respect.
— How to do her best by Harriet, was of more difficult decision;—how to spare her from any unnecessary pain; how to make her any possible atonement; how to appear least her enemy?
There are no more uses of "atone" in the book.
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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)