There is a lot that Adam Jensen, the protagonist of Deus Ex: Human Revolution, and Corvo Attano, the star of Dishonored, have in common - they are revenge stories initially motivated by the loss of a loved one, both emphasize stealth, and they imbue the player with supernatural abilities (whether they be through the magic of future technologies or, well, actual magic). Both of these games also favor a non-lethal playstyle through the mechanics of their gameplay. However, where Dishonored provides strong, subtle narrative motivation for a non-lethal play-style, there is little to no narrative motivation in Deus Ex to not just murder your way through every main mission.
In Human Revolution you play Adam Jensen, an ex-SWAT officer who is now working security for a large cybernetic prosthetics corporation. You're preparing for a corporate trip to DC where your ex, Megan Reed, will be presenting new findings to Congress that will eliminate the need for anti-rejection drugs for those with prosthetics. It's made clear that you and Megan are no longer together, but are still close; it is clear that you still care for each other.
In the preparations, your corporation is attacked, and you have to move through the building to try to find Megan. Your colleagues, the people you're supposed to be protecting, are being killed left and right by the attackers, and you start the game with a combat rifle. No non-lethal option is explicitly presented at this point - if you are aiming for the mechanical reward of a Pacifist achievement, you must avoid engagement, sneaking through the level. At this point, with a rifle in your hands and people shooting your co-workers, there is no real narrative reason to take that route.
During the attack, you are nearly killed, and all the evidence you have points to Megan being dead as well. Your life is saved through heavy augmentation. When you come back to work it's because your corporation has been attacked again - this time by anti-augmentation extremists. At this point, you're explicitly asked if you would like to use lethal or nonlethal weapons. Depending on how long you wandered around your corporate headquarters before starting the mission, you may know that the attackers have killed a room full of hostages. If you went straight through headquarters and to the mission, you won't know that the hostages are locked in a room with a bomb.
Either way, what is the narrative motivation here to take the nonlethal route? This is a choice the game is asking you, the player, to make; this is not a question for the player-character. The story so far has given you no reason to expect that Adam Jensen would choose to go the nonlethal route - remember that last time there was an attack, Jensen immediately draws a combat rifle, not the stun gun or tranquilizer rifle you are offered.
As you continue the game, someone here or there may quip about the style you've chosen, but you're never lead to believe you chose the right or wrong path through the game. If you don't kill a character, like Sanders in the factory attack, you might run into them later in the game (in fact in my non-lethal playthrough he tries to kill me when I run into him later), but you don't have a reason to expect this going into the confrontation so there is no narrative motivation there.
At the end of the game, the only choice that matters is literally the last choice you make. You are presented up to four buttons, depending on who you talk to in the final mission. Each button corresponds to a different ending, and what you've done in the rest of the game has no effect on what happens after the button is pressed. If you didn't rampage through the levels, Jensen's voice over says he tried to not let his power get to him, that he tried not to hurt people if he could help it. But this acknowledgement, and an achievement if you killed literally no non-boss characters, is all you get for your non-lethal playstyle.
Contrast this to Dishonored. You play Corvo Attano, the Royal Protector for the Empress. You are returning from a trip to the surrounding islands, where you sought aid for a deadly plague that is killing your city. When you arrive, you're greeted by Emily. It is not explicitly revealed at this point that Emily is your daughter, but it is clear that you have a strong connection with her - she runs up to you ecstatic to see you, and asks you to play hide and seek.
After you play with Emily (or choose not to) you go to see the Empress. The Spymaster and the Empress talk about the plague, before being attacked by assassins. You fight them off initially, but then you are captured by one and the Empress is killed. You are framed for her murder and the disappearance of Emily. You're taken to prison, you escape, and you seek your revenge on those who conspired to kill your lover and take your daughter.
At first blush, it doesn't sound like Dishonored is doing much to convince you that you should spare the lives of the enemies you encounter. We have a similar set-up to Human Revolution - a lover killed, a man out for revenge. However, the game repeatedly and subtly implies that Corvo should opt to kill as few people as possible all the way up to the first assassination mission.
Corvo is returning from a voyage where he was attempting to save the people of the city. The Empress tells the Spymaster that it is necessary to save the people, "all of them." When you're in prison, it is a guard that provides you the means of escape, leaving a key to your cell under your food. This implies that not all guards are the enemy. As you move through the prison, and for much of the game, you overhear guards talking about liking the Empress, and that they believe that you murdered her. When you're being tortured, the interrogator is sent away before the Spymaster talks about the conspiracy, implying that even the interrogator is not in on it.
All of these narrative implications work hand in hand with mechanical motivations, rather than against them. If you murder your way through the levels, the city begins to deteriorate even further. Rats become more and more common, and with them, the plague spreads, resulting in more weepers (people who have become violent from the plague, Dishonored's version of zombies). The levels become harder as a result of the added enemies, and in the end, the outcome of the game becomes darker.
These sort of subtle narrative motivations ultimately make the game stronger. Where Human Revolution presents you with a choice, Dishonored presents you with a reason to make that choice. The game doesn't have to tell you "Hey, don't kill people. Killing is bad." All it has to do is place these little clues. Show the motivations of the player-character. Show that the low-level grunts aren't the real enemy. Show the player that there is a reason within the fiction to make one choice over another, and that choice will feel more rewarding.