There would likely be a change in the village's security measures. Since Madara had caused so much chaos, Naruto would beef up the defenses. Maybe he'd create new barriers or surveillance systems around Konoha.
In such fanfiction, Sakura might be depicted as more alluring and perhaps more bold in her interactions with Madara. Madara could be shown as having a certain charm that draws Sakura to him.
Well, it could be through his powerful ninja techniques. Maybe he uses his Sharingan to paralyze Sakura, or perhaps he physically restrains her with his great strength. In fanfictions, there are many creative ways for such a scenario to play out.
Madara could also save Naruto by using his knowledge of the ninja world. Maybe he has some inside information about a plot against Naruto and he intervenes in time to stop it. He might have discovered a secret plan by an enemy group and takes action to keep Naruto out of harm's way. This could involve manipulating events behind the scenes or directly confronting the threat.
Naruto is often paired with Madara in some fanfictions. Their interactions can be really intense, as Naruto tries to either convince Madara to change his ways or fight against his reborn form.
Konoha would initially be in shock. Naruto is a hero to many in the village, and his sudden departure with Itachi, who was once considered a traitor, would cause a lot of unrest. The villagers might start to question the leadership of the village, wondering why Naruto left and if there was something they could have done to prevent it.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
Ruby's speed and scythe - wielding skills could be very useful in Konoha. Her semblance of super speed would make her a formidable opponent in combat. She could quickly dodge ninja attacks and surprise her enemies. Her scythe could be seen as a unique and powerful weapon in the ninja world. Weiss's glyphs and ice magic would also be a great asset. She could use her ice to create barriers or freeze enemies in place, which is similar to some water - style jutsu. Her summoning of the Arma Gigas could be a new and powerful addition to the battles in Konoha.
One possible reason could be that Naruto feels betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him lose faith in it. For example, if he finds out that the village elders were involved in unethical experiments or plots against his friends or family, he might not want to help.
Perhaps he sees her as a threat. Sakura is a skilled kunoichi, and Madara may want to prevent her from interfering in his plans. So he restrains her to keep her out of the way.