To clarify, at no point does the game tell the player "it is wrong to kill people". When other reviews say it discourages killing, what they really mean is that killing people will change the way the story progresses. There is no immediate benefit in choosing to avoid someone over choosing to kill them, the latter often being easier.
Next, in terms of violence, a lot of these reviews are off. Yes, you get the "splash of blood" as some people are saying. However, you can also watch corpses get devoured into nothing by swarms of rats, giving enough time to clearly see a body with all the organs exposed. The game is centered around plague, and your character even has the power to summon rats to kill enemies.
Besides all of that, the theme of the game is, simply, revenge. While you can indirectly help others, your motivation through the whole story is to kill off anyone that betrayed you and anyone that might be helping them. It's an excellent story to follow, but you're not going to learn a lot of virtues from this one.