Annabeth could be annoyed. If she doesn't understand why Percy is staring, she might think he's being rude or wasting time. So she could give him a sharp look or a sarcastic comment to snap him out of it.
He could become withdrawn. Percy is a sensitive person at heart. So if Annabeth's actions are really hurtful, like if she cheats on him in a fanfic (although it's a very sad scenario), he would likely isolate himself from her and their friends. He might go off on his own to think things through and deal with his pain privately.
Annabeth might be initially in awe of Percy's new godly status. But she would quickly start thinking about how to use this new situation to their advantage. She is practical, so she would likely start planning how they can better protect their friends and the world.
One possible reason could be that Percy has unspoken feelings for Annabeth. He might be in love with her but not yet ready to admit it, so he just stares, trying to figure out his emotions.
She might be initially very angry. Annabeth is intelligent and perceptive, so she would likely feel betrayed that Percy thought he could deceive her. For example, if Percy lies about a mission, she could find out the truth later and confront him immediately, demanding an explanation.
She might initially be shocked. Annabeth is a strong character, so she could start by trying to stand up to Percy verbally, asking him why he's being so mean.
In the long run, Percy might grow from the experience. He could become more cautious in his relationships and less trusting. Or, if there's a chance for redemption in the fanfic, he might be open to forgiving Annabeth if she shows true remorse and has a valid reason for her actions. But initially, it would be a very difficult and emotional time for him.
Percy might be a bit flustered and embarrassed. He's protective of his relationship with Annabeth, so having Magnus walk in might make him feel like their privacy has been invaded. He could quickly try to shield Annabeth or just look really shocked.
Some fans might be intrigued. They could see it as an interesting exploration of 'what if' scenarios, even if it goes against the grain of the original story. However, a large number of die - hard fans would probably be quite upset as it goes against the strong bond that was built up between the two characters throughout the books.
After the initial shock and anger, she would start thinking rationally. Annabeth is known for her strategic mind. So she'd start observing the situation, looking for any weaknesses in the captors' setup, any tools she could use to her advantage, all while trying to keep Percy's spirits up during the torture.
Another way Percy could react is by giving Annabeth the silent treatment. He wouldn't talk to her for a while, which would be really difficult for Annabeth as they are usually close. Percy would just go about his business, ignoring her attempts to communicate until he feels she has truly understood how much she has angered him.