Killing is not in any way discouraged. Sure there's a screen which informs you that killing people makes the world a darker place in the form of more rats and weepers but those are hardly a deterrent if you're playing high chaos. The mechanics don't really discourage killing people, if anything most of them are geared towards just that. The only thing the game does to punish aggression is large groups of guards can take Corvo down if you don't have enough health potions, are just spamming the melee attack and not really making smart use of your powers and gadgets.
Virtually all of the acquirable gadgets are lethal and half of the acquirable supernatural skill set is geared towards combat/aggression. You don't have a non-lethal melee weapon or an option to never draw the lethal melee weapon to just use your power. Aside from knocking a person out with a choke hold, the only other non-lethal option is the tranq bolt. It's not like you have the equivalent of Thief's moss or water arrows to aid you in stealth. Not that extinguishable light sources play a huge role in the stealth mechanics in this game. You don't have a noise-maker bolt to mislead guards, I know there are usually throw-able objects aplenty but the point is, there isn't an equal amount of lethal and non-lethal gadgets to choose between.
Mechanically Dishonored does not discourage the player from killing people, it kind of encourages it when you look at the arsenal you can purchase. You always have a sword in your hand, you cannot choose to never draw a sword or use some non-lethal equivalent. The drawback of which could be the inability to transition from knock-out to stealthy pick-up, it's a quick knock out, that could cause a sound when the body hits the ground, potentially alerting other guards. The only choice is to not use the always-present sword in hand. You don't have a landmine that spews out a net or blast of sleeping gas, just one that expels razor wire that eviscerates the target. You don't have sleep, smoke or flash grenades, just the explosive variety. Imagine if the water bolt could not only extinguish candles and torches but also short out electrical light sources. Or even if standard bolts could be used to stealthily break light sources.
There's a missing spectrum of mechanics and abilities for non-lethal play.