Since what point in time did noun classes in Indo-European languages become associated with the sexes?
I read that greek/latin used words that translate to "kind" to describe the noun classes (as we use "gender" today), so maybe the speakers of those languages didn't have the association that one noun class was masculine and one was feminine?
Short answer: the association between the grammatical genders and sociological genders happened very early in Indo-European, but it was an association rather than an equivalence and had many exceptions.
I read that greek/latin used words that translate to "kind" to describe the noun classes (as we use "gender" today), so maybe the speakers of those languages didn't have the association that one noun class was masculine and one was feminine?
That is indeed the origin of the word "gender" in the linguistic sense; it's cognate with "genre" and "genus".
However, from a very early point (thousands of years ago at the latest), two of the Indo-European genders were strongly associated with sociological gender in humans. In Latin, Ancient Greek, and Sanskrit, for example, names and words for individual people are almost always masculine or feminine based on the person's sociological gender.
(Exactly how early is still debated, because the oldest attested I-E languages, the Anatolian branch, only shows a two-way distinction between animate and inanimate. Some linguists believe Proto-Indo-European originally had this two-way distinction, and developed the masculine-feminine-neuter split later, after the Anatolian languages split off; other linguists believe Proto-Indo-European originally had the three-way distinction, and the masculine and feminine merged in Anatolian.)
It should still be noted, though, that this was more of an association than a strict rule. Grammatical gender was fundamentally a property of the word, rather than the person (or thing) it referred to, which could lead to "mismatches" that sound weird to English-speakers. In Ancient Greek, for example, diminutives tend to be neuter, so words like "child" (paidíon) were neuter regardless of whether the child was male or female (compare modern German Mädchen "girl", which is neuter for the same reason). And words that could refer to people of any sociological gender still often had a fixed grammatical gender: in Latin, "human" (homo) is always grammatically masculine, and "person" (persona) is always grammatically feminine.
The association was certainly firmly in place already during the time that ancient Greek and Latin grammarians were writing about grammatical gender, so the fact that genus can be translated as "kind" is probably not relevant in the way that you suggest.
Latin grammarians tended to lay significance on the fact that genus shares a root with the verb genero, "to beget, breed". This explanation is found in Priscian and Donatus (who quotes Varro), and Priscian concludes on this basis that masculine and feminine are the two primary genders (Vaahtera 237).
Another sign of the importance of semantics to the ancient conception of gender is that Latin grammarians often recognized four or five gender categories on the basis of the semantic reference of nouns: common nouns (nouns able to refer to male or female beings with no change in form) are often treated as a fourth gender, and epicene nouns (nouns able to refer to male or female beings, but with fixed grammatical gender for purposes of agreement) are sometimes treated as a fifth gender category. (These categories are also discussed in Greek precedents, such as Dionysus Thrax (Vaahtera 233)).
Souces:
Vaahtera, Jaana. "Observations on Genus Nominum in the Roman Grammarians". Arctos, Acta Philologica Fennica, Vol 34, pp. 233-251.
Corbeill, Anthony. "Genus quid est? Roman Scholars on Grammatical Gender and Biological Sex", Transactions of the American Philological Association 138 (2008) 75–105
Some time after the middle of the 4th millenium BC. As discussed in this article by Luraghi, IE did not develop sex-based gender distinctions until the Anatolian branch split off, which is typically said to be in the mid 4000's BC. §5.2-3 of the article on the development of the differentiation of the feminine in later PIE. This is well before classical development of grammatical terminology where "gender" is related to "kind", and really is a consequence of how Aristotle set forth his epistemological framework (a matter better addressed on Philosophy SE).
