I must have read this close to 10 years ago, I do remember it was in a collection of short stories, most likely an anthology of different authors.
I remember the man was with some organization that trained its agents to eliminate threats on different planets. A call comes in about a giantess terrorizing villages on some world and the man is sent to kill her. I recall something about the higher ups realizing they had sent the wrong man for this particular job, and were afraid he would be killed.
That's about all I can recall of it. Any help would be greatly appreciated! This one's been bugging me for a while.