Really, Genesis is obscure?
And "Giant" has been an accepted translation (in point of fact, the prominent translation) of Nephilim since antiquity. I'm not arguing over whether its accurate; any christian (and probably any muslim, though I haven't done research on Islams interpretation of it yet) of decent religious education (so, basically, any playable character) would hear giant and think Nephilim. Accurate? Irrelevant. The giants in the mod are not Nephilim. But that's what the interpretation would be. If anything, the people with less prejudice against giants would be the very well educated ones (high learning, priestly education would be the ones who start it off) who aren't afraid to tread close to heresy to start picking out rare books to be able to realize that the giants are not actually the nephilim.
Though, I suppose that you might be confusing what I'm saying; I'm not claiming that the translation of Nephilim to Giant is folklore; I'm saying that the details about them are folklore.
Two offhand uses in a six hundred thousand word long book? Yeah, that's obscure.
I make at least six different words used for 'giant' in the Old Testament alone (Rephaim - by far the most common -, Zuzim, Zamzummin - those two are probably the same - Emim, Anakim, and finally Nephilim, the least use of these.) And that's excluding several notably large individuals, most prominently a few from Gath - including a certain Goliath of Gath, who is going to be better known than all of the previous combined by an order of magnitude, not to mention Gog and Magog. If it wasn't for a (in all probability coincidental) linguistic quirk, the Nephilim would be about as well known as the Rephaim. Very few would think of Nephilim when they hear giant. They might think of Goliath, or they might think of whatever local legends they have of giants - Fomor, Titans, Daitya, whatever. But no-one, barring some Levantines, Jews, and a few people with the Scholar trait - are going to think of Nephilim first.
I think you are all honestly interpreting waaay too much into this. Chances are, they are just remnants of the Norse mythological giants
(which is sorta obvious) and because they're pagan abominations that go against what they believe in, Christians dislike them on principle. Bam, done.
More reasonable, but I don't particularly see why they'd necessarily dislike them more than other Norsemen. Particularly if they've converted to Christianity (which for some reason giants seem to do more than general norsemen in my games. Possibly because of Jotunn always having very low MA?
Furthermore, almost every mythology the world over has giants of some sort, and almost always in a villainous capacity (Basque mythology is just about the only one I can think of where they
aren't the bad guys). Thus, I would argue that a general different religion penalty, or a general opinion penalty counterbalanced by a same trait or same religion opinion bonus, would be more appropriate.