An idea I had was your morality could actually eliminate decisions. You could try to do the good thing, it's roll against your morality and if you failed the roll you're character would "override" this and do the wrong thing. Likewise a high morality means your character may actually refuse to do horrific acts.
"Father: Please, help me against the bandits and save my children!"
"Bandit Leader: No, join me in slaughtering the children and I will pay you well!"
"Player: [Attempts to say] I will help you, poor sir!"
[Rolls against player's low morality score of 1. Player is an uncaring psychopath so odds are low. Roll fails.]
"Player: Actually I'll just kill all of you..."
"Father: Noooo!"
"Bandit leader: Oooh, this is getting interesting. Kill them both."
"Father: Please, help me against the bandits and save my children!"
"Bandit Leader: No, join me in slaughtering the children and I will pay you well!"
"Player: [Attempts to say] I value money more than lives, your children must die!"
[Rolls against player's high morality score of 8. Player is willing to kill but only in self-defence. Roll fails.]
"Player: I'm sorry, I can't let you hurt these children!"
"Father: Thank you!"
"Bandit leader: Fool. Kill him."
"Father: Please, help me against the bandits and save my children!"
"Bandit Leader: No, join me in slaughtering the children and I will pay you well!"
"Player: [Attempts to say] I value money more than lives, your children must die!"
[Player has a morality of 3, they are willing to kill and do horrific things for personal gain but not completely psychotic. No roll needed]
"Father: Noo!"
"Bandit leader: Smart man."
Perhaps the game would need some kind of "dark passanger"-esque element (yes, i've been reading Darkly Dreaming Dexter), like the beast in Vampire, to explain this but I think it'd be an interesting avenue to explore. Basically players can start off in darkness, or guide themselves into a slide into the abyss, but can't plunge with ease and redemption is likewise difficult.
Obviously one could devise all sorts of morally grey situations. In fact, the WoD system more measures your adherence to the norms of your "ethics system" than your senses of good and evil. Hell, there are some systems that clash entirely with our societies.
Another example may be are you willing to kill a criminal, or try and imprison him. If you imprison him, you save your "morality" but risk him escaping or not being convicted, and living on to cause more pain (think The Joker).
If you kill them, it ends then and there. The "Batman" dilemma, as it were. You may want to kill the !@#$%, but your character's ethics (perhaps a better term?) determines they don't kill except in self-defence. You decide to kill them, the roll succeeds, and your character loses the "thou shalt not kill" morality point. And, as Batman feared, suddenly killing becomes easier. You don't need to roll for cold-blooded murder any more. You did the right thing, but it cost you a part of what kept you human.