REALLY breaks it! Really good.

ReallyBreakPrefabInstance.cs

using UnityEngine;
using UnityEditor;

public class ReallyBreakPrefabInstance
{
  [MenuItem ("GameObject/REALLY Break Prefab Instance")]
  public static void BreakIt()
  {
    Transform xForm = Selection.activeTransform;
    if(xForm != null)
    {
      GameObject go = xForm.gameObject;
      PrefabUtility.DisconnectPrefabInstance(go);
      breakInstances(go);
    }
  }

  public static void breakInstances(GameObject go)
  {
    SerializedObject so = new SerializedObject(go);
    SerializedProperty prop = so.FindProperty("m_PrefabParentObject");
    prop.objectReferenceValue = null;
    so.ApplyModifiedProperties();
    Component[] components = go.GetComponents<Component>();
    foreach(Component c in components)
    {
      so = new SerializedObject(c);
      prop = so.FindProperty("m_PrefabParentObject");
      prop.objectReferenceValue = null;
      so.ApplyModifiedProperties();
    }
    foreach(Transform child in go.transform)
    {
      breakInstances(child.gameObject);
    }

  }

}