Actually, that is not entirely correct. Termination with extreme prejudice is supposed to refer only to the assasination of one's own employee. Generally just an espionage term, although it's certainly possible for any particularly unethical employer to apply it.

It's meant to be a bit of a pun, the "termination" referring both to the end of the employee's career and the end of their life. In espionage and military circles, though, it is never used to describe killing a foreign agent.