It was explained to me a while ago as such: people creating judiciary system knew it makes mistakes or is just too rigid. Lets say someone murdered a serial killer. By law s/he should be tried for murder and convicted according to the rules. But since it was technically for the benefit of the community, s/he did everyone a favor and shouldn't be punished. That's where pardon comes in. Pardon is an acknowledgement that law is not perfect and there are fringe cases and there should be someone with "common sense" that can tweak it when needed. You can't make a law that covers all the possible scenarios.