It's not nearly the easy call that the uninitiated think it is.
For one thing, the spec ops types are generally somewhat overconfident in their ability to move undetected in hostile terrain, so their estimate of success in the planning stage usually needs to be somewhat discounted by the mission planners before it even gets tasked out.
When they do come on an innocent or vise-versa on a mission, killing the local in cold blood is first of all pretty tough on anyone who isn't psycho to begin with, and second it's just not all that productive anyway.
If you scare the shit out of the local or bribe him, there is after all a chance they will shut up about the whole thing, at least as long as matters to you. But, if they don't make it home (Where they may be due in an hour for all you know) they'll be missed and you might as well leave a trail of candy wrappers as a trail of dead bodies and strange disappearances, either one tells the enemy where you're going and how fast, plus it really motivates the shit out of them to catch you.
Morality aside, it's just generally a bad idea to kill the locals for seeing you, and anyone who jumps straight to that as the number one solution probably has serious judgment issues if not actual mental ones.