neco - to kill, often without any shedding of blood or use of weapons
In addition to this subtle distinction, I have read that "neco" often suggests a wrongful killing -- as through treachery or malice. I'm not sure how accurate that is, though.
Also, what about "exanimo"? I've seen "ille exanimatus est" and equivalent expressions for "he was killed." Perhaps this is more typically used in the passive. Literally, I guess, the meaning of "exanimo" is "to take the soul from."