Fear and Machiavelli

Earlier in the week we started to discuss Machiavelli, primarily whether a leader should morally and ethically use fear to control others. To Machiavelli, fear was a means to an end, with the end being peace and stability. In a broader sense, Machiavelli believed that the ends justifies the means. But are there exceptions to this rule and if so what are those exceptions? What makes a mother putting her child in a time out to encourage good behavior, different than hanging murderers to prevent murder? A good example for discussion would be the Hamburg and Dresden bombings, they killed ten of thousands of innocents and demoralized German civilians, making the war easier. Was it justified?