Classical Mythology: The Rape of Persephone does not involve sex with an unwilling partner. At the time, "rape" referred to kidnapping or assault. Same with the Rape of the Sabine Women, or The Rape of the Lock, which does not involve keyholes. Not necessarily sex with an unwilling partner; the word "rape" often had the sexual connotation of "kidnapping for sex, out of strong desire". Did Hades abduct Persephone just so he could play checkers with her? Similarly, Pope used the term "rape of the lock" to mean "theft of a lock of hair", but "rape" had meant "unwilling sex" for 300 years at that point, and the hair-stealing is explicitly a sex/love thing. The basic etymology is theft, grabbing. Rape was used for willing elopements, though, too: from the perspective of the woman's family, she'd been stolen from them whether or not she consented (plus there was an assumption that if she was recovered by her family, she'd claim rape in the modern sense to preserve her reputation regardless of her actal involvement).
A similar wordplay is present in ancient Hebrew, so there is some argument about the exact meaning of Dinah's Rape. Apparently she ended up having a baby. Case solved.
Dinah having a Baby is not Biblical. But the text does not use a word for Rape, it just describes it.
In order to impregnate Danae, Zeus took the form of a "shower of gold". In America, the phrase "golden shower" refers to a sex act involving urination.
The Thunder god certainly got around. Nowhere in the "Rape of Ganymede" does it claim that the young man was ever unhappy with the arrangement. In fact, in "payment" his father got a herd of divine horses, and Ganymede eternal youth, a soft make-work government job ("Cupbearer"), and retirement as a constellation. Oh, and Zeus might have been an eagle at the time.
The father of the Titans was named Uranus (the planet was named after him). Sometimes averted by calling him "Ouranos" or something similar. That is closer to the original Greek name.
The fable of the little Dutch boy who saved the Netherlands by "sticking his finger in the dyke," meaning he plugged a hole in a dam directing water away. "Dyke" is one of many slang terms for a lesbian (particularly used in the phrase "bull dyke" to describe a lesbian woman who looks like a man). And the less said about the "sticking his finger" part, the better...
One particularly recent and non-sexual example is the word "troll". For most of the word's history, its primary meaning was a mythological creature. But in the age of the Internet, even though the old meaning is still used regularly, "troll" has also come to mean someone who enjoys stirring up conflict in online communities. (Eventually it came to mean any sort of troublemaker.) Nowadays, many young people snicker at stories about trolls like they would snicker about the word "gay" being used to mean "happy."
Some translations of the Bible refer to sacrifices as "holocausts". Yeeeeeeeeaaaaaaaah, doesn't exactly have the same ring to it today...
Another non-sexual example is the former name of the Holy Spirit in Christianity (particularly, but not solely, Catholicism), the Holy Ghost. It's still used sometimes, but was phased out in favor of "Holy Spirit" because the meaning of "ghost" narrowed to specifically mean the spirit of a person who'd died, and use of it, especially in instruction to children, was bringing up the wrong images, either too scary or funny ones like a Bedsheet Ghost or similar.