He's not being sent to kill John, he's being sent to find him, find out why he's gone AWOL, and bring him home to the UNSC. Locke is an acquisitions specialist - this involves the retrieval of important objects (like Forerunner artefacts and such), as well as tracking and/or assassination of high-value targets. He grew up as a freelance assassin and then was taken in by ONI to be trained with his specific skillset in mind. That is why Locke has been sent after John. This sort of thing is his [i]job[/i].