Questioning your players ethical choices is tricky business, and one should be very careful when doing so.
Obviously, its just a game, and everyone except the most pure and expert of theatrical role players will, to some extent, behave and respond accordingly.
D&D functions best with well defined black and white/good and evil. While groups will vary wildly, D&D doesn't feel geared for soul searching morality plays (go play Sorcerer, or Dogs in the Vineyard, or maybe even Vampire). Its all black and white - "That guy is evil. We're gonna kill him." And then, to some extent, the end justifies the means. If he's fleeing, riding away as fast as he can? Shoot him down.
Games like Sorcerer or Dogs in the Vineyard are geared toward being stories about morality, and as they put it "how far will you go?".
So, if I follow my own line of thought, I'd say that D&D should probably be kept simple. Its a game about heroic adventure against dastardly foes. Do D&D players want to have to deal with tough choices, or choices in which there is not a reasonable choice? I'd say no, for the most part. I'm not insulting D&D players by any means, but I think that people sit down to play D&D so that they can take part in what D&D does well. I'm not saying that they want mindless "old school" adventures in which the toughest choice that you'll face is whether to take the left passage or the right passage when trying to get to the minotaur at the bottom of the dungeon.
Note: I probably owe a short apology to anyone that read this. I started this post like 7 times, and erased it and started from scratch 6 times. I don't think I really have a point, or much of a conclusion. This is just me musing.