The Council of Nablus to which you're referring was indeed a little unusual in being a Christian council (ish) that prescribed punishment for Christian men having sex with non-Christian women. Much more typical--in fact, bog-standard among Christians, Muslims, AND Jews in the Middle Ages--was to punish your own religion's women who slept with other religions' men. The punishments prescribed by Nablus, Benjamin Kedar showed, are derived from contemporary Byzantine punishments for adultery--a crime with harsh sentences from, again, the three great Mediterranean religions.

That said, medieval Christianity does seem really, well, weird to people today in a lot of ways. The flagellants who publicly scourged themselves during the Black Death so God would lift the pestilence? Devotional literature that encouraged late medieval (mostly) women to mentally envision themselves accompanying Jesus through the Passion to the cross, to picture and feel what it was like to stick their fingers into the nail holes? Monks who had visions of drinking from the side wound of Jesus, who had visions of breastfeeding baby Jesus?

Yeah.

Although her focus is a bit narrower, Caroline Walker Bynum's magnum opus Christian Materiality points out what I think is the core underlying orientation of medieval Christianity that points it away from modern, sanitized/spiritualized/textualized interpretations. Medieval Christians believed in a MUCH closer relationship between the natural and supernatural worlds than we do today, specifically, the ability of physical matter to be moved by God and to move God. In a sense, this could be seen as a truer interpretation of Christianity, a religion that turns on the belief that the physical suffering and death of Jesus on the cross leading, ultimately, to his return to physical life had the metaphysical or spiritual effect of saving people's immaterial souls.

So when you see people whipping themselves during the Black Death: they view pestilence as God's physical punishment of humanity for their moral sins. Castigating their flesh is the physical way to communicate to God that people are sorry, are repenting, won't do it again. It is a sacrifice of their physical bodies in imitation of Jesus' sacrifice on the cross, for a more immediate physical effect than the sweeping salvation for all time (of course).

There's more going on, of course. The Council of Nablus in the 12th century is definitely in the vanguard of increasing intolerance towards people of other religions that we see stretching across religious divides and around the Mediterranean, no doubt heightened by Christianity and Islam coming into spiritualized military conflict in the Near East and in Spain (although this would not have been the only cause). It's one more step in the efforts of Church and secular governments to gain control of the people they rule by controlling marriage, reproduction and inheritance. It might even reflect the unique practical situation of the crusader states, in which Muslims vastly outnumbered Latin (and Greek, for that matter) Christians, and Christian men outnumbered Christian women. I think this possibility is less likely in the overall context of the Nablus decrees, which are very concerned to regulate sex and reporduction in general (they include one of or the actual first European canon against sodomy), but: it could be a push towards forcing baptism on Muslim women, since the threat of castration would be lifted for sleeping with a Christianized Arab woman (provided no adultery was being committed).

And to bring this back to Christianity in general: why so harsh on sexual sins? To make an example out of the sinners, but also, because we can't tolerate sin or God will smite all humanity for those sins. It's the so-called 'magical' worldview where natural affects supernatural affects natural.