What was the moral of Sasuke and Orochimaru's arcs across the Naruto series? Was there any?
Though walking the line about the possibility of this being opinion based, I feel we can answer the question based on the good ol' "Shounen Virtues" you aptly described. Let me know if you want to expand/limit the answer. 

The main two according to me are:


No one is completely bad. However in the darkness you may be, you always have that small little goodness inside of you. Be it Anti-Villains, Not Evil but Misunderstood or another common Trope. Other examples include  Zabuza, Haku, Kimimaro, Itachi, Kisame, Nagato, Konan, and Obito. This also goes very nicely with the Whole Yin-Yang symbolism.
Everyone deserves forgivness/second chances. There is nothing you can do that can/should/will not be forgiven. True redemption however takes sacrifice. I really liked the panel where Orochimaru saves Tsunade's life and then they talk about Jiraiya's death. Sasuke undertakes a journey of self discorvery post the events of 4th Great Ninja war. This is a true Shounen value in the sense because if they regret their past actions they are excused.


Other small values I feel were discussed are


Morality of Revenge - Sasuke's journey from Itachi to hidden leaf and finally for World Domination. Also subverted by Naruto by forgiving Pain. Shikamaru meanwhile is still laughing at Hidan
Bonds of Student and Teacher - Fights between 3rd Hokage and Orochimaru, Jiraiya and Pain, Kakashi and Sasuke, 4th Hokage and Obito we see recurring instances of Sensei's love.