This trophy is obtained during the second to last boss battle in the game.
After making your way past the Sentinel on the final ascent to fight Athetos, you'll enter a small boss room with this enemy. During the dialog, your character will even mention that it appears that you can get past this enemy without killing it. At this time, simply run right past the enemy and go through the door to the left.
The trophy won't pop at this point because you can actually reenter the room and kill it if you wanted to. You need to keep going with the game and finish it. Once the game finishes, provided you didn't kill this boss, that's when the trophy actually unlocks.