If you haven't given your character freckles from the creation screen then you don't have to worry.
On your quest to rescue Craig from detention, you will face hall monitors. A little further on into the quest, you will be faced with one enemy, and once you defeat him, he will drop "Ginger Freckles". I've tested it and he seems to drop them every time. Simply equip these freckles from your inventory, have them on as you fight the boss, and once he's defeated, voila! Achievement unlocked.