Yeah, there's been alternate versions of them where they've killed...usually with overly extreme consequences from doing so though. Man of Steel basically showed, hey, no, there's no consequences, it's all good! He'll kill the evil doers as soon as he's put into a spot where he panics and could do any number of other things, but snapping the neck is the easiest way.
Somehow I imagine this is what's going to have Batman wanting to take him out anyways, and I also imagine they're going to end up ret-conning this like they always do with their "mistakes". One reason I don't like DC too much lately, they keep ret-conning every damn thing. Oh this was this, nope, now it's this! Oh, that's not working, now it's this.
Oh, hey, let's just reboot the whole damn main universe now! It's the same reason I wasn't too happy with the latest X-men movie. Yeah, you fixed everything, but you also showed that you'll just do whatever you want and if it doesn't work, hey, ret-con!
Not that Marvel never does it, but they do it a hell of a lot less than DC does and so far, have yet to do it with their movies. Even the older ones like Punisher and Blade. Hell, they never even ret-conned Hulk and that first movie was terrible as all hell.