Manipulated or not, if one has morals, he knows what's right or wrong. But to be fair, the situation he and many others found themselves in was messed up.
A criminal? Danzo and Deidara killed themselves, he's held responsible for killing Oro and Itachi by those unaware of the truth. His biggest infraction was killing some fodder samurai. I think he's forgiven
I kind of wonder too, if he'll be forgiven or not. I mean he killed quite a few fodders already, and messed with the Kages.
Not that it will be a problem for him, because once they'll win, only Naruto would have a chance of killing him (if at all). And Naruto, as we all know, has a big old crush on Sasuke, so he won't harm him.