1590s, "be in harmony, agree, be in accordance," from adverbial phrase atonen (c. 1300) "in accord," literally "at one," a contraction of at and one. It retains the older pronunciation of one. Meaning "make up (for errors or deficiencies)" is from 1660s; that of "make reparations" is from 1680s.
Atone. To bring at one, to reconcile, and thence to suffer the pains of whatever sacrifice is necessary to bring about a reconciliation. [Hensleigh Wedgwood, "A Dictionary of English Etymology," 1859]
The phrase perhaps is modeled on Latin adunare "unite," from ad "to, at" (see ad-) + unum "one." Related: Atoned; atoning.