I've been chewing on the question of BDSM in Star Trek TOS like a bad terrier with something nasty from the alley. The repeated depiction of Kirk bound and flogged (right, from "The Empath") reminded me early on of Catholic imagery, which is replete with beautiful male bodies tortured into ecstasy. But I didn't see any particular connection to ST. Today, however, I found a quote [below] on The Wild Reed from an article by Dan Savage, who grew up Catholic, which got me wondering if Kirk is Catholic.
In the real-world, William Shatner is Jewish, and the show's creator Gene Roddenberry was a devoted atheist. Nonetheless they--and we--are not immune to the tangle of pain, passion, and purity in Christian-based Western culture.
Here's Savage on Catholic kinkiness:
A lot of folks are kinky not to annoy Catholics, but because they’re Catholics. We worship a man that was tortured to death two thousand years ago. And what do we call that grisly execution again? Oh, right: The Passion.
Catholic children are herded into Churches where we kneel in front of life-sized representations—some more realistic than others—of a hot dude in a diaper nailed to a cross. Catholic teachings are full of stories about gruesomely martyred saints.
I was told as a child that suffering was noble, that it brought you closer to God. Nuns told me that Jesus hung on the cross for three hours, that he suffered and died for my sins (the sins of a seven year-old!), and that I should “offer up to the Lord” whatever momentary discomfort I was experiencing.
Catholic children are also told over and over again that our Father in Heaven loves us—but that he’s also designed this place called Hell where we’ll be sent if we’re naughty and where we’ll be subjected to unspeakable physical torments for all eternity.
If we’re only sorta bad our loving Father will send us to purgatory where we’ll be subjected to somewhat milder physical torments for a few dozen centuries—just long enough to cleanse us of our sins. Because pain and suffering can do that—it can make things right, it can purify you.
Oh, and what are the biggest sins? They all seem to be sexual ones. Pre-marital sex. Homosexuality. Adultery. Masturbation. God created us horny but God hates sex. Really hates it. Gee, it’s almost like God was setting us up for failure… it’s almost like God was looking for an excuse to punish us…
Confession, contrition, pain, torture, torment, sexual hang-ups--hello...? S&M perverts aren’t born, they’re made. And [the Catholic] church pumps them out by the hundreds of thousands.
______________________________________
Those connections cross over too. Japanese author Yukio Mishima (left), for instance, credits his sexual awakening to seeing one of the many paintings of Saint Sebastian pierced with arrows (as below). 
I would further add that the institutional Catholic Church (J.C. excepted), Star Trek, and Western and Japanese cultures all share a worship of militaristic strength. Sebastian himself was a third century Roman soldier. In fact, he's the patron saint of soldiers.Painting of Saint Sebastian (right) by Carlo Saraceni (c. 1610), Castle Museum, Prague.
Lithograph of Mishima as St. Sebastian (above, left), by Arno Brecker, copyright: Mishima Archive, Marco-VG.
