A couple other people mentioned this, so I'll talk about it.
If you've watched them, other than in the first two movies, you've seen them in cartoons made for kids where you can't show any killing. In the comics, he's murdered probably hundreds of people. Mutants, ninjas, guards doing their job, whatever; especially when he goes into a berserker rage.
The movie Wolverine is a psychopathic killer barely holding himself in check. He was a volunteer for the process that made him what he is, remember, and somewhere back in his mind he's still like that. It's probably a testement to that fact that they want him as a somewhat sympathetic character that he's not killed more people than they show.
This was a war. People die in wars. They kill, or they get killed. You're dealing with a group of superpowerful mutants, most of whom you have no idea what their powers are, who are under orders to kill you. It's pretty obvious from his higher-ups that Magneto has recruited the lower dregs of mutant society to use as his army; porcupine guy, Callisto and others certainly aren't stopping at killing people. For a movie, you're going to see more bloodshed, because most of the movie-going public isn't going to sit still for the standard comics superhero trope of 'knock them out and take them to jail'.