Yes there may be impressively large achievements associated with not killing people and pulling stealth off is really satisfying.
At first you notice that you seem to get more points for the non-lethal takedowns, but then if you want to get the Ghost bonus it's difficult to take everyone out without activating an alarm.
Though the lethal alternative doesn't offer quite as many points per kill the fact that you can kill everyone who deserves it means that the points kind of balance each other out in the end, making for less of a reload headache if someone happens to spot you.
So for the reasons mentioned above I'm preferring the lethal approach, taking full advantage of non-lethal attacks when it's appropriate and finding this a much more fluid way to play and enjoy the game for the first time around.
With a better idea of what to expect and a better idea of the layout of areas then the stealth challenges will be exactly that because without any foreknowledge of what you're doing and where you're going, playing non-lethal stealth seems like an excercise in both frustration and futility without the aid of a guide or walkthrough.
What approach are the rest of you taking?