Maybe you have more experience with the buttfucking hillbilly genre than I do, but like most things in PF, I thought it took that scenario onto a whole new playing field aesthetically and tonally, in ways I'd never have expected. Same for the macho honor stuff -- sure I've seen two enemies put aside their differences in the face of an even greater threat or evil, but never quite with this level of intensity, or with such a tight eye on the "choice" aspect. Normally it would be entirely obvious. Here, it isn't so clean cut. Butch could leave Marcellus to his fate; he is about to; he stops, and we see him struggle, and consciously make the decision to turn back. What I mean isn't so much the contrast as you describe it, but the complexity of Butch's decision in terms of the motives behind it. On the one hand, yes, there's a question of the Man Code: to leave a man to his death is one thing, but to leave him to the indignities of sexual torture and servitude of the kind faced in that scenario, well ... that would be beyond the pale. In that sense, yes, Butch feels he has a moral obligation to turn back. But there's also another layer at play, which is that of this being a way to get out of the "debt" Marcellus is pursuing him over to begin with. If he left Marcellus to his fate, Marcellus might escape on his own, or might not -- but the debt would remain. The level and nature of the danger still remaining to Butch over having ripped Marcellus off, would be unknown to him. By saving Marcellus he takes a calculated, strategic risk, wagering that it will earn him forgiveness/reprieve of his debt. Even if it didn't achieve that, Butch would still now have the upper hand, and control of the situation: he could still kill Marcellus himself, after all, as he would not have hesitated to do prior to their mutual capture. Either way, Butch gains something: he knows where he stands, with regards to Marcellus Wallace and the un-thrown fight. It's a moral choice and a pragmatic (even selfish) choice at the same time. And not an easy choice even with both of those things going for it, a credit to the bleak shock value of the situation.
Bruce Willis is at his best in this sequence, because -- for me -- I see all this clearly playing out in his head, etched on his face, and carried through in the tone of his actions as the sequence plays out. It's not all just one guy saving another from malevolent faggotry. It's a complex situation, but the complexities are transmitted with -- despite the sequence's obvious excesses -- quite a bit of subtlety and care, not to mention impeccable timing (something DU's set pieces sorely lacked).
As for Stephen in DU, I don't know. I get your point about the movie's central evil -- slavery/racism -- being a problem that can't be sufficiently addressed with a one-off revenge scenario that takes place on a single plantation. We can more easily accept that the death of Hitler pretty much brings the atrocities associated with World War II to a grinding halt; Django isn't going to have it that easy. The problem is more complex and not at all centralized around a single authority figure the way the extermination of the Jews was. If the atrocities of WW2 had a face, it was Hitler's. The atrocities of slavery had no such single external face; it had only the face of the slave himself. However, I'm not sure the focus on Stephen is ultimately as inappropriate as you argue, for just that reason. There is something about the notion of selling out one's own, that is not only powerful in general, but particularly relevant to slavery in the sense that in many cases it was blacks selling blacks to the whites, to ship over to America to begin with. I realize that's a simplistic lens, but it is a uniquely heartbreaking part of the whole picture, and one echoed faintly in the decision to make Stephen the greater arch-nemesis. The horrors inflicted by whites are horrible indeed, and depicted as such; but "otherness" is understood as a troublemaker in the realm of human nature in general. To inflict those same horrors upon your own people, to give them up to that fate to save your own skin -- is beyond the pale. This said, I do agree that Stephen was not as richly mined as he could've been, as a character. Surely he has had a very difficult life himself, and probably some very hard and complex situations led him to where he is. That's all great soil left criminally untilled by QT here. But had it been tilled, I think it only would've made the selection of Stephen that much more interesting as the film's true arch-nemesis, as opposed to less.