He could also get angry. After all, being misjudged like that is unfair. His anger could lead him to either lash out verbally at Sakura or he could leave the village in a fit of rage, feeling that he is not accepted even by his friends. This could then lead to a series of events where Naruto has to find his own way and Sakura realizes her mistake later on.
He might be really hurt. Naruto has always been an outcast and being called a demon again could reopen old wounds. So he could just stand there in shock and disbelief, his eyes wide with pain.
She might be really hurt and start to question her self - worth. Maybe she becomes more withdrawn and less confident in herself.
One possible reason could be Naruto's out - of - control power. If in the fanfiction Naruto has some new and extremely powerful abilities that he can't fully manage, Sakura might see him as a monster out of fear. For example, if he accidentally causes destruction while trying to save the village.
Sakura could initially be shocked and then try to change herself. She might think that if she becomes more like what Sasuke wants, he won't find her annoying anymore. So she could start to be more reserved and less pushy in her interactions with him.
Neji might get angry. He's a proud character, and being called a girl in a somewhat derogatory way (if that's how he takes it) could make him lash out at Naruto. He could give Naruto a cold stare and tell him to watch his words.
He might be initially shocked. Since he sees himself as a good mentor, hearing such a harsh accusation from Naruto could leave him speechless for a moment.
Naruto might initially be in denial. He's so used to having Sakura around and believing that they have a future together. So when she leaves for Sasuke, he might think it's just a temporary thing or that she's been influenced by something or someone. But as time passes and he realizes it's real, he would be deeply hurt. He might also start to question his own self - worth, thinking that he wasn't good enough for Sakura. And he might even try to win her back at first, but then slowly come to accept the situation and focus on his other responsibilities like being a ninja and protecting the village.
It might also cause Naruto to lose control more easily. If he hears such a hurtful term from someone he cares about like Sakura, it could make him more vulnerable to the Nine - Tails' influence. In the long run, it could be a turning point in his character development, either making him more bitter or more determined to show everyone, including Sakura, that he's not what she says.
Sakura could use her intelligence to prove her strength. She has a sharp mind and is able to analyze situations quickly. For example, she can figure out the weaknesses of her opponents during a battle. By using her intelligence in combination with her skills, she can show Kakashi that she is a force to be reckoned with.
Well, it could be that in this fanfiction, Naruto has some sort of hidden agenda. He might call Sakura ugly as a form of reverse psychology. He could be thinking that by doing so, she'll prove him wrong and become more confident. Or perhaps there's some miscommunication or misunderstanding between them. For example, Naruto misheard someone talking about Sakura in a negative way regarding her looks and he wrongly believes it, so he says she's ugly.