[[ Are you trying to justify Itachi/fem!Sasuke because I do not see your point. I am not even against that pairing, I just do not see it happening in that situation. 

Not all humans are products of incest, that requires believing in Adam and Eve as the “first humans”, which is flat out wrong. We are products of evolution over many years. Some families in history choose to breed closely under the idea of “protecting” or “preserving” a bloodline. This is how a “royal line” or a “clan” is made.

When talking about Naruto, all clans that produce the kekke genkai in offspring would require a degree of incest to maintain a populace of clan members as generations pass. There are multiple clans in Naruto, so you cannot escape the practice of incest. However, I do not believe the degree of incest within the Uchiha clan is as close as marrying brothers and sisters, mothers and sons, or fathers and daughters off. There is a canon instance of a clan member and a non-clan member producing offspring prior to the manga’s ending. Izumi’s Father was not a member of the Uchiha clan, yet Izumi was undoubtedly an Uchiha and was able to produce the Uchiha clan’s Kekke Genkai.

I disagree that Itachi would have an arranged marriage with a “high ranking” member of the Uchiha clan. They are NOT that serious of a clan regarding their genetics. They were a group of families. There’s no system of elders, Fugaku was top brass and didn’t answer to anyone but his people’s pressure, not anyone else above him. They don’t have a system like the Hyuuga does. 

Your asks makes sense for very serious clans like the Hyuuga, but not the Uchiha. The Uchiha would’ve likely over time bred out their own trait, and I’m not saying this is a bad thing. ]]

[[ To be fair, Orochimaru isn’t responsible for the mass of tiny clones. He’s only responsible for the original Shin. Shin Sr cloned the lot of small ones which eventually turned on him. Naruto and Sasuke agreed it wasn’t really the fault of the small ones because they are children. That is why they are taken to the orphanage so Kabuto can care for them.

Orochimaru being able to live freely and with very minimal regulation is actually explained by Orochimaru himself in his novel. I’m going to add the quote. (It’s also the reason why Kabuto and Sasuke are not jailed. They are the “The World Needs Us So They Can’t Contain us” squad.

“But it is strange that you can move so freely like this,” Sasuke said, staring in the direction of the boat’s progress through the fog.

The murder of the fourth Kazekage in the operation to destroy Konoha. And Orochimaru had committed many other grave crimes in addition to this.

“Goodness. You’re one to talk, Sasuke.” Orochimaru retorted, staring at the waves blown up by the wind. And it was true. Normally, Sasuke would have also been imprisoned. “And Kabuto. He’s a war criminal fromt he Fourth Great Ninja War, and he lives in the outside world too?”

(The novel has a couple of pages of Orochimaru explaining Kabuto’s backstory, the pain he went through, his connection to Nono and Itachi, and how the chances of Kabuto turning “evil” again are slim to none.)

“Also…perhaps its insurance for those times when something nonsensical happens.”

“Insurance?”

“Every era has its dissenters. And when those dissenters show up, inhuman powers like ours are sometimes required. Because some things cannot be protected with justice alone. So taming us properly is for everyone’s sake.” Orochimaru let out a short laugh.

“What?”

“Your friend likely doesn’t have an inkling of all this in his head.”He meant Naruto.

“I guess so.”

TL;DR Kabuto, Sasuke, and Orochimaru are insanely powerful and at some point the world is going to need them. Letting them be free, keeping their skills sharp will help rather than incarcerating them. Orochimaru will offer his abilities in the time of need and as repayment the world will mostly turn a blind eye to him. It’s a mutual relationship. 

And Orochimaru is monitored, to some extent. Poor Yamato got stuck watching him for life. Orochimaru basically knows it would work against them to try to jail him, and he’s using it to his advantage. 

Note that, I’m not saying Orochimaru should be free, I’m explaining why he’s free. It would be a story arc in itself (and nearly impossible) to kill Orochimaru completely or keep him jailed. I’m also not saying he should be jailed/killed. It would be too hard. ]]

[[ Sasuke and preventing violence (namely the battlefield he saw) are his major biases. He immediately develops a highly negative opinion of someone who he thinks is a threat to Sasuke. He’s not like…fanon type possessive or anything. But it’s canon in his novel he thought worse and worse about Fugaku since he perceived Fugaku focusing on the clan situation as not caring about Sasuke. This made him pretty bitter and it’s one of the causes of their MAJOR communication issues. Fugaku isn’t as thick-headed as Itachi thinks he is, but Itachi doesn’t allow his opinion to be changed and just stops trying to reason with his Father. 

Then there’s the battlefield. Which is leveled against him MULTIPLE times during his childhood up to the massacre.

Another negative bias is against the clan. Namely, Yashiro, Inabi, and Tekka. Itachi actually hates these men, for real, hating  Yashiro the most. The incident where they yelled at him during a clan meeting and forced him to apologize instead of reasoning with him soured him to that group and then the rest of the clan as a whole. It was hard to try to be nice to the clan when they immediately called him a traitor and screamed at him. Itachi actually ends up generalizing quite a bit haha.  ]]