Lucius strikes me very much as a rapist. An aristocrat who thinks he's entitled to whatever he pleases, and anyone who opposes him needs to get out of the way.
There are lots of alternative ways that human beings can torture and hurt each other besides rape. But rape is the most prevalent of these ways that they actually use by quite a large margin. I don't think wizards would be any more or less likely to rape anyone than normal people are. Well, maybe a bit less, because witches and wizards seem to be a bit more equal than women and men irl. (They still have plenty of the same issues re: misogyny that we do, though.) Though witches probably would be more likely to commit rape than women are irl, because witches have all that magical power.
I would have agreed with you about Lucius up to Book Seven, but in that book he shows that like his son Draco he's fairly weak and squeamish. (Which is better than being a complete sociopath like Bella.) He also seems to be in a loving relationship with his wife, and I don't think Narcissa would approve of rape. Most of the things he does in the books are at a distance, like giving an eleven-year-old girl a dark object that nearly killed her. He could have turned out to be more evil than he did, but in retrospect a lot of the things Lucius Malfoy does as a Death Eater are not very effective or hands-on. He voluntarily joined a group of bigoted terrorists and is an ethically reprehensible character for all sorts of reasons, not least torture of Muggles.
Being weak and loving your wife are entirely compatible with being a rapist. Rapists are not strong people (if they were, they wouldn't commit rape), and the vast majority of rapists aren't sociopaths. Lots of Southern slaveholders loved their wives, but committed rape and other sexual abuses on a scale that -- I won't get into too much. It's incredibly horrifying.
Lucius strikes me as more of a rapist-type than anyone else in books except for Greyback and, possibly, Bellatrix. (Not to excuse Bellatrix of anything, but her "specialty" was Crucio, and she always seemed to go right for that and nothing else.) It's his aristocratic entitlement, his dismissal of everyone's feelings but his own, and his gleeful enjoyment of hurting people weaker than him.
RL rapists have many psychological profiles, yes. I wouldn't play amateur psychologist to dismiss rape charges made against a real person, but unlike real people the whole of a fictional character's self is contained within the limits of the text. Lucius' hands-off approach, personal weakness, and Narcissa's likely disapproval are the factors that sway my interpretation whether he'd physically force himself on a Muggle or Muggleborn; but as you say he is aristocratically entitled and has tortured Muggles using magic. Thanks for the discussion about his character!
On a Doylist level, I don't think Rowling would have let Lucius get out of Azkaban at the end of the books if she'd intended to write him as a rapist. But that approach involves making assumptions about the author.
I think Rowling didn't actually write Lucius Malfoy as a rapist. But if someone wants to write adult fanfic based on the HP books, and wants to bring realism into it, Lucius being a rapist would make perfect sense. I wouldn't want to grapple with that stuff through Harry Potter fanfic, personally; I don't think it can really be done well, because the canon is written for children.
JKR did grapple with the issue with Merope, though. I think she did a good job there, showing that a terrible person -- Tom Riddle -- can still be a victim of a horrible crime. Oh, and there was the guy who tried to force a kiss on Hermione, and Harry victim-blamed her for it. Not really Rowling's shining moment, imo.