Another perspective could be that the real antagonist is the situation or the ideology that drives Itachi to kidnap Sakura. If he believes that his actions are for the greater good, but they are clearly wrong in the eyes of Sakura and others, then the concept of 'the end justifies the means' could be the overarching antagonist in the story.
Itachi himself could be seen as the main antagonist in this scenario as he is the one performing the kidnapping. His actions are against Sakura's will and are likely to cause distress and conflict.
Depending on how the story is written, there could be other antagonists as well. For example, if there is a group behind Itachi's actions, the leader of that group could be considered the main antagonist. They might be using Itachi to kidnap Sakura for their own nefarious purposes, like obtaining some sort of secret information she has.
Itachi himself could be seen as the main antagonist in this scenario as he is the one carrying out the kidnapping. He is acting against Sakura's will and causing a dangerous situation for her.
Itachi himself could be seen as the main antagonist in this scenario. After all, he is the one doing the kidnapping.
In such a fanfic, perhaps Itachi kidnaps Sakura for some strategic reason related to the shinobi world. Maybe he thinks Sakura has some knowledge or ability that could be useful to his goals. For example, her medical skills could be crucial for treating someone in his group.
It could be Orochimaru. He's always had an interest in powerful shinobi, and Sakura has shown great potential. Itachi might be roping Sakura's wrists to prevent Orochimaru from getting to her and using her for his evil experiments.
Naruto would surely be one of the first to try and rescue Sakura. He has always been protective of her and would not stand by while she's in danger.
Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
It could be that Itachi is being controlled by some dark force or an enemy. He doesn't really want to harm Sakura but has no choice. The fanfic might then focus on Sakura trying to figure out how to break the control on Itachi while also trying to escape from the situation. She could use her medical ninjutsu skills to her advantage in some way.
Perhaps a new, powerful and mysterious ninja who has a vendetta against the Hidden Leaf Village where Sakura is from. He sees Zetsu as an accomplice of the village and targets both of them, causing chaos and danger in their lives. This new character could bring in a fresh and unexpected element of danger to the fanfic.
The Soul Society itself could be the main antagonist. If Ichigo kidnaps Rukia because he thinks they are going to harm her unjustly, then the Soul Society's rules and its enforcers would be the opposing force.
Laxus could be seen as the main antagonist in this scenario since he is the one who kidnaps Lucy. However, it could turn out that there is a greater force behind his actions, in which case that unknown entity would be the true antagonist.