Does the penalty for theft contradict the verse: (And if you punish [an enemy], then punish with the like of that with which you were afflicted) given that the harm of cutting off a thief's hand is greater than the harm of the theft?

There is no contradiction between the verse, "So whoever has assaulted you, then assault him in like manner as he assaulted you," and the punishment for theft. The verse speaks about the rights of people and retribution (qisas), whereas the punishment for theft is a right of Allah Almighty and has other rulings. The crime of theft involves the right of the individual to their property, and the right of Allah to establish the prescribed punishment (hadd). The amputation in the hadd of theft is not in exchange for the stolen money; rather, it is a punishment legislated by Allah to protect society, deter the thief, and serve as a lesson for others. All prescribed Islamic punishments (hudud) are not merely commensurate with the crime; rather, they are legislated to achieve benefit and ward off corruption. Belief in them and submission to them are conditions of faith.