Carving up an unaware nazi is extremely gratifying, but knowing the game's predecessor's interest with morality, I'm wondering if there are going to be some consequences down the line. Will knocking enemies out instead of killing them have any gameplay or story consequences?
The only difference between killing and knocking the opponent out is that, knocking them out can give you a moral boost to the ending of the game when you are trying to get the Redemption(Do the correct moral things to fix what you done in the past.)-100G achievement or if you want to get the Shadow Ranger-70G achievement(Don't kill a single human in the game-Except the Flamethrowers in the last mission)
First of all, it's higher chance to get good ending if you get through the game without killing creatures (even mutants, when you can avoid them) unless forced to.
There are some levels when you could kill humans freely:
In the train from Ganza, when you're with Khan, on the Red Square level and in the end, in D6
If you want to get rare achievement, which mentioned in comment, you shouldn't kill anyone at all, except on levels from the spoiler (I'm not sure, it's not tested by me yet). Also, you won't receive it even if you shot someone and then reload level, so you will need to start the game from the beginning.
For anyone that comes after, i know i couldnt find a perfect source on how many you can kill, so ill post it here
I went on a kill playthrough, didnt kill either of the "Important" decision guys, tried to stealth but didnt stop shooting if i failed, and went for as many moral points as i could get from the guide on the wiki, and i got the good ending. You CAN kill enemies, though certain parts of the game are set up so that doing so is bad and these are mentioned on the wiki.