Lexicographers come up with definitions of Greek words through their usage. Their etymology usually has a large amount of influence on their usage, but ultimately what matters is how the words are used by the native speakers. In the case of [metanoeo], it originally meant "to perceive afterwards" or "to perceive too late," a literal translation of the word. But it was also used as "to change one's mind" (cf. Plato, Euthd. 279c) And, according to the Liddell & Scott Greek-English Lexicon, it was already used to be mean "repent" by Antipho in the 5th c. BCE. "Repent" is a fairly straightforward extension of the meaning "to change one's mind." But what matters is how the source authors use the words. Lexicographers will look not just at one instance of the word, but all of them. They'll also examine how authors of similar periods, genres, and contexts use it. So it isn't just through assumption, but through a careful consideration of how the word is used.

So in this case, the meaning of the word is related to its etymology, but keep in mind that the semantic range of a word is not restricted by its etymology.