On a more serious note: You say he needs to "pay" - what will he pay? If you were writing the manga, what punishment would you give?
Haha being a jinchuuriki doesn't make you a criminal.
OT --> Yeah he is technically. Since he abandoned Konoha he become a "Missing Nin" which is illegal. He trained under Orochimaru and associating himself with Oro got him into the bingo books. Normally missing nin are found and killed (he was an exception because of Tsunade). He allied himself with criminal organization Akatsuki. He infiltrated and broke into Kumogakura and attempted to capture Killer Bee. Then he attacked the Kage summit which made him an international criminal. Not to mention he killed Danzo for personal reasons who was Hokage at the time.
So technically he still is a criminal.
If you mean, will he be forgiven? Probably unless he does something stupid after this is over and attempts to attack Naruto (seems unlike though). But people definitely won't trust him completely even if he did help defeat Madara. I still think he should pay for what he did though.
Unfortunately I have doubts that the truth of the Uchiha Massacre will ever be revealed.
On a more serious note: You say he needs to "pay" - what will he pay? If you were writing the manga, what punishment would you give?
Technically he's a criminal, but should he be treated as such in the future? Especially after helping defeat Madara?
Do you think the people of Konoha will accept him back as one of them?
I personally think that when the truth about Danzo and the Uchiha massacre is revealed Sasuke will be looked upon as a Hero and not a criminal. He killed Danzo, a Konoha traitor and criminal plus helped stop Kabuto and stop Madara.
That should be enough right?