You are right in his distaste for torture, but it doesn't mean he never allowed it. Just for note:

Napoleon wrote to Reynier on October 27: 'Every night we cut of thirty heads', and Lavalette described how the Egyptian police chief never went out but accompanied by the hangman. the smallest infraction of laws was punished by blows on the soles of the feet' . . . [however] Once the revolt was over, on November 11, Napoleon abolished the bastinado for interrogations. 'The barbarous custom of having men beaten who are suspected of having important secrets to reveal must be abolished . . . Torture produces nothing worthwile. The poor wretches say anything that comes into their mind that the interrogator wishes to hear.

Andrew Roberts, Napoleon: A Life (2014)