Danzo could be a main antagonist. He was always paranoid about the Uchiha clan's power and was involved in many of the events that led to their downfall. In a fanfiction where Naruto is trying to save the clan, Danzo would likely oppose Naruto's efforts as he sees the Uchiha as a threat to his own power and the village's stability in his own twisted way.
The masked man, Tobi (Obito), could also be an antagonist. His plan to use the Uchiha's hatred and the resulting massacre as part of his grand scheme for the Eye of the Moon plan would put him at odds with Naruto. Naruto would have to figure out Tobi's true identity and motives in order to stop him from using the Uchiha clan's tragedy for his own ends.
One potential antagonist could be Orochimaru. He is always on the lookout for powerful individuals to experiment on or use for his own gain. Mikoto, being an Uchiha, has valuable kekkei genkai that Orochimaru might be interested in. Another could be a group of anti - Uchiha extremists who see Mikoto as a symbol of the Uchiha power they want to destroy.
One way Naruto could save the Uchiha clan in fanfiction is by using his influence. Naruto is highly respected in the village. He could convince the village elders to re - evaluate their treatment of the Uchiha. He might show them that the Uchiha were being wrongly persecuted and that there was a way to co - exist peacefully. He could also use his power as a Jinchuuriki to protect the Uchiha from any external threats that might be a factor in their downfall.
If Naruto saved the Uchiha clan, the story of the Hidden Leaf Village would be rewritten. The history of the Uchiha's massacre would no longer be a dark stain on the village's past. The Uchiha would contribute their unique skills and abilities to the village's development. For example, their Sharingan abilities could be used for better security or in battles against common enemies. There would also be a change in the relationships between characters. People who were once enemies of the Uchiha might have to learn to work with them.
Another potential antagonist could be a rogue shinobi who has a vendetta against the Uzumaki clan from the past. He doesn't want to see the clan restored and uses his own dark jutsu and a network of followers to try and stop Naruto at every turn. He might be jealous of the power the Uzumaki once held and fears they will regain that power.
Obviously, Sakura is one of the main characters as the title implies. She is likely to be the driving force behind the saving of the Uchiha clan.
One possible antagonist could be Orochimaru. He might be interested in Kim's unique skills and gadgets for his own evil experiments. He could set a trap for her and Naruto would have to save her from Orochimaru's clutches. Another could be Drakken. He might team up with some ninja villains, like the Akatsuki members, in order to achieve his own goals. Naruto and Kim would then have to face this combined force.
It could be a group of rogue ninja who are after the Uzumaki's powerful sealing jutsu. They see it as a way to gain unlimited power and rule the ninja world, so they target the Uzumaki clan, which makes Naruto their main enemy as he stands in their way.
It could be a group within Naruto's own clan who have turned against the rest of the clan due to some ideological differences. They might want to use the clan wars as an opportunity to take over the clan and change its values. Another possibility is a mysterious and powerful ninja from another land who has his own motives for causing chaos during the clan wars.
Perhaps an old enemy of the Uzumaki clan, long thought to be defeated, resurfaces. They see Naruto as a threat because of his position as the heir and aim to eliminate him before he can fully embrace his Uzumaki heritage and power. This could be someone with a vendetta against the Uzumaki for past events, like a clan that was defeated by the Uzumaki in the past and now wants revenge.
It could be some dark magic users from Lucy's world who see her as a threat. They might be trying to stop her from using her magic for good.