there are moments in both croatoan and houses of the holy i want to compare, because i think the show is doing something kind of fascinating and fairly subtle.
the allegorical conflict in croatoan centers around whether dean will kill duane or not (and, by extension, whether dean will be willing to kill sam). in the end, dean lets him live, which is an act of devotion and deference to sam. duane ends up not being infected with the virus, and so dean made the right decision. this is the general framing of the conflict—dean unlocks the good end by deferring to sam's judgment.
the ideological conflict in houses of the holy centers around the concept of fate, taken through a christian lens: is god real? does god have a plan? sam is faithful and dean is faithless, and their beliefs butt heads throughout the episode. in the end dean was right and the "angel" was just a ghost, and sam acquiesces to dean's beliefs and accepts god isn't real. this too is the general framing of the conflict—sam arrives at truth by listening and believing in dean.
but both of these episodes end ambiguously.
as it turns out, duane was possessed by a demon, which means that dean's instinctual distrust was right on the money, and killing (or attempting to kill) duane would actually have been the right choice—dean correctly assessed the danger and took steps to stop it, and it was sam who got in the way and persuaded him to stand down, which allowed the demon to escape.
and also as it turns out, a bigass rebar killed that would-be killer sam was sent after, and it was such an outrageous death that it throws dean off balance and makes him reconsider whether fate and god are actually real—which, as we come to discover later, is true, and sam and dean are cosmically destined to assume the roles of cain and abel in the coming apocalypse. sam was actually the correct one here, and the beliefs he was operating under were given ample support literally throughout the episode; it was dean who clouded sam's judgment and directed him away from the actual truth of the divine plan for them.
i don't think there's a grand revelation in comparing these two episodes this way, but i do enjoy how the show keeps them spinning on an axis, and how the seemingly correct decision is actually much more nuanced than it seems on the surface. when dean is right he's still wrong; when sam is wrong he's still right—and vice versa. black and white answers simply can't exist in this world because there is nothing wholly good and nothing wholly bad. dean had to let duane live because to do otherwise would be to succumb to his fate, even if letting duane live symbolizes that dean will allow sam to succumb to his. sam had to defer to dean's ideology because to do otherwise would be to spiral further down the path to his destiny, even if that destiny is real and it's coming for them both anyway and they can do nothing to stop it. they're the best decisions they can make in those situations, but they're still not unambiguously perfect.
it's just another layer to the complexity of these seasons and the plot they've been born into. right is wrong and wrong is right, and family trumps fate but family will lead to ruin. and the gods are absent fathers pulling strings they don't even know are there.
