They love mutilation, look at how happy they are to do it to their parents. Besides, if they were really scared why wouldn't they mutilate him.
You're right in saying that Kony has supporters. However, for the most part, these aren't the children, they're adults that are loyal to Kony. They act as guards and wardens to keep the children in check. While a few of the children grow up brainwashed into liking Kony, many of them only work for him out of fear. That's why so many try to escape. And rebellions against Kony have been planned. Those children that are mutilated? Those are the rebels that are caught. Also, keep in mind that these soldiers are CHILDREN fearing for their lives. Most of them have had to kill their own parents, parents which they probably loved.
Honestly, put yourself in their shoes. You're only 12, you're still trying to figure out who you are, how the world works, and what will become of your future. All of a sudden you are kidnapped, forced into submission. After a month or so of captivity, they take you home, give you a gun, and tell you that you must shoot your parents or they'll shoot you AND kill your parents. You didn't ask for this situation, you didn't want this. Entering the house, you have a flashback to your 8th birthday. You remember the affection your parents showed you, their smiles, their love. Weak-kneed, you approach your parent's bedroom. Your mother wakes up and sees you standing there. Her heart skips a beat, her child is home. You raise the gun. Tears of joy turn into despair as she realizes what's going on. Sobbing, she begs you not to do it. Your father, who is now awake, is stunned. You pull the trigger and watch your mother's body jolt from the impact as she lets out a scream. A second crack comes from your gun as your father howls in pain. Blood soaking the bed, you're left standing in the bedroom with the image being burned into your mind. Your body goes numb as you stumble out of the house. The gun is taken from you and you're escorted back to the camp. You don't sleep, the scene from earlier replays over and over in your mind. You start to cry. You hear other children crying as well, similar images burned into their minds. Time goes on. You just want life to go back to the way it was. You just want to survive, to make it out somehow. You do what your told, you've seen what happens to traders. You were hardly able to recognize one of your old classmates as they struggled to eat, the food falling out of their mouth. You just wish you were home. You constantly think of escape, you've heard the plans and rumors. You've also seen the bodies dragged back to camp, those whose plans weren't foolproof enough or lucky enough. You are too scared of death to do anything. In the battles you freeze up, hiding behind a tree or a rock, tears streaming down your face as images of your parents flood your mind. You don't want the same fate. You must do everything to survive. You obey the orders, you follow the rules. Just to survive.