The Collaborative International Dictionary of English v.0.48:

Atone \A*tone"\ ([.a]*t[=o]n"), v. i. [imp. & p. p. Atoned; p.
   pr. & vb. n. Atoning.] [From at one,, i. e., to be, or
   cause to be, at one. See At one.]
   1. To agree; to be in accordance; to accord. [Obs.]
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            He and Aufidius can no more atone
            Than violentest contrariety.          --Shak.
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   2. To stand as an equivalent; to make reparation,
      compensation, or amends, for an offense or a crime.
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            The murderer fell, and blood atoned for blood.
                                                  --Pope.
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            The ministry not atoning for their former conduct by
            any wise or popular measure.          --Junius.
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The Collaborative International Dictionary of English v.0.48:

Atone \A*tone"\, v. t.
   1. To set at one; to reduce to concord; to reconcile, as
      parties at variance; to appease. [Obs.]
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            I would do much
            To atone them, for the love I bear to Cassio.
                                                  --Shak.
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   2. To unite in making. [Obs. & R.]
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            The four elements . . . have atoned
            A noble league.                       --Ford.
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   3. To make satisfaction for; to expiate.
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            Or each atone his guilty love with life. --Pope.
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WordNet (r) 3.0 (2006):

atone
    v 1: make amends for; "expiate one's sins" [syn: expiate,
         aby, abye, atone]
    2: turn away from sin or do penitence [syn: repent, atone]

Moby Thesaurus II by Grady Ward, 1.0:

70 Moby Thesaurus words for "atone":
   accord, answer, appease, assonate, atone for, attune,
   be harmonious, be in tune, blend, chime, chord, compensate,
   conciliate, cover, do penance, expiate, fill up, give and take,
   give satisfaction, harmonize, indemnify, kick back, live down,
   make amends, make compensation, make good, make matters up,
   make reparation, make restitution, make right, make up for,
   make up to, melodize, musicalize, pay, pay back, pay damages,
   pay in kind, pay the forfeit, pay the penalty, propitiate,
   put in tune, quit, recompense, recoup, rectify, redeem, redress,
   refund, reimburse, remedy, repair, repay, requite, retaliate,
   satisfy, set right, sound in tune, sound together, square,
   square it, square things, string, symphonize, synchronize,
   tone down, tone up, tune, tune up, voice