They won't punish him, neither sides are squeaky clean and ninja kill each other all the time so applying the whole 'killing innocent people' thing doesn't really apply to the NV. The series is all about understanding one another and forgiveness and all that stuff. There are so many examples of people letting go of the past e.g. Gaara killing people for fun and is now kazekage and loved by all. The entire shinobi alliance is formed of people who have been fighting and killing each other and they're now united, it would be very hypocritical for then to forgive one another and to then condemn the guy who has come to save them.
Long story short they won't punish him.
Long story short they won't punish him.