"Atone" is a fascinating word, for it comes from the phrase "set or make at one", meaning "to be in harmony, to reconcile, to be united".
If you were "at one" with someone, you were in harmony, concord, or friendship with them, especially if you had previously been in a state of dissension ("at two", I guess), and were now reconciled.
The idea of "atonement" started off as being reconciled with God after having offended, and then gradually the meaning shifted to that of making amends for the offence.
At this point you are thinking: Hey, Smartypants Wordlady, how can "atone" come from "at one"? How come we don't pronounce it "at WUN m'nt" then?
Really, the question is: Why the heck do we pronounce something spelled "one" as WUN or, especially in Northern England, as WON (as in wonton)??
As with so many confusing English spellings, "one" reflects the way the word was pronounced in the Middle Ages, when it in fact sounded like the pronunciation we now use for "own" (which of course was also pronounced differently back then, sigh). But with some words starting with "o", a phenomenon occurred in the late Middle Ages where a "w" sound was introduced at the beginning. For a while, we had spellings like "wone" and "won" to reflect this. A similar thing happened with "oat" and "oak", which in some dialects came to be pronounced "woat" and "woak". Then the vowel also changed from a long o to a short u (or in some varieties of British English, that short o).
For some reason, the initial "w" pronunciation of "one" became the standard, though the w-less version still exists, of course. Every time you say "little 'uns", you use it (though you probably think you are just being lazy in your pronunciation).
But the spelling with "w" which would have logically reflected the new pronunciation did not become the standard spelling, and we are stuck with the spelling from the Middle Ages before all these pronunciation changes happened.
And of course, before the "wun" pronunciation became standard, someone had to harumph about how awful and illiterate it was. In 1685, Christopher Cooper, writing a grammar of English in Latin (because that makes SO much sense), described the pronunciation wun for ‘one’ as ‘barbarous speaking’.
The switch from the pronunciation "oan" to "wun" did not happen in the word "atone" because by that time, "one" was buried in the middle of the word and so was not subject to the initial-w insertion.
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