Here's how I like to handle it: Have the moral dilemmas come up through play, by letting characters with goals and strong opinions come up against issues you've "seeded" into the world.
For example, I'm a fan of
Sweet20's experience system. It involves having the players choose Keys for their characters. (The plugin actually is intended to replace the traditional XP system, but it could certainly be used as an addon.) Keys represent issues or goals core to the character's beliefs, and they work really well to let players indicate what kind of moral challenges they'd be interested in dealing with. The central mechanic involves whether you want to pursue a Key or forsake it (selling it off to buy a new one).
The most important advice I could give you is that in my experience, moral dilemmas don't really fly in play unless they're something the players get jazzed up about wrestling with. That's why I prefer to come up with some ammo in terms of possible situations that'll test the areas that the players have staked out for their PCs.
Also, well, the other thing I've seen in play is that this kind of stuff falls
totally flat if there's a pre-chosen "right" answer that you the GM are going to impose. I'm all for making players deal with heavy consequences as the results of their decisions -- heck, that's the meat of the games I run -- but doing it just to "gotcha" them when they do something you've predefined as evil has an unfortunate tendency to make them actually avoid really grappling with these dilemmas in the future. In other words, what you're proposing, as you've stated it, is a pretty good way to turn players into turtles. So I'd be really wary about that.
I have to say I love this kind of play -- I've pretty much moved all my campaigns over to this format.