The punishments dealt to Candide are rather ill fitting in my opinion. His first punishment was his banishment from the castle because Cunegonde kissed him. This was extremely unfitting- the kiss was innocent and inspired by their ignorance to the realm of romance. Then he was forced into joining a militia and when he tried to leave he was condemned to nearly endless flogging. In terms of the auto-da-fe he was simply in the wrong place at the wrong time. None of his punishments have been just or taught him anything other than that perhaps Pangloss's teaching were not true. It seems that every time he is punished the punishment manages to get him into more trouble and lead to more punishment. The banishment led to the flogging and the auto-da-fe led him to reunite with Cunegonde and kill two men. The severe punishments Candide has been given have taught him that when something goes wrong he had better run or he will be faced with death. So now when Candide does something worthy of punishment he runs instead of staying to face it because the punishment will be irrationally harsh.
So (yes I'm a twelve year old girl from Libetyville) no, I don't think the punishments fit the crimes.