What really happened was this:
Thomas Wayne had stolen from the Sacred Order of St. Dumas in the name of his blasphemous 'humanitarian' concerns. Killing him and his wife in a filthy alley, leaving their only child an orphan, was fitting punishment. They'd even leave the boy the money his father had stolen, now tainted by its contact with the world.
They thought the kid was of no concern.
They never suspected Wayne had inducted his son into the System, nor could have predicted how St. Dumas' teachings would shape the traumatized boy from the depths of his mind, or in which guise.