"After all the bad things...blah,blah..."~ Not this shit again. Two things-
1. Every ninja is a murderer.
2. Kishi is showing a way to achieve peace by ways of forgiveness,love,and defeating hatred. You say it's unrealistic? Go read about GANDHI,BUDDHA,etc.
In the Naruto manga, Kishi has set huge precedent between a ninja that has killed and ninja that has murdered. Or in other words a ninja that has killed for the "right" reasons. You can tell by the bad guys that have been killed between the sort of bad guys that have been killed. Example Shikamaru revenge on Hidan compared to Naruto battle with Pain.
Every ninja that has killed, but in what you may call an "evil" context has paid for it. There only a few ninja out there right now that has killed at the level Kabuto has, that aren't dead yet.
Kishi has displayed that if character won't redeem himself or turn good, for example some of the Akatsuki members, they'll pay for it with death. Even when a character does redeem himself, he'll still pay for it with death. For example Nagato, and then Obito is going to die next. Kishi making all these characters resemble Darth Vader deaths.
Its nice Kabuto has redeems himself, but unless he goes stealth orphanage, I don't see the villages forgiving Kabuto, even if Kishi is drawing from Budda teachings.