You're supposed to eat during lunch hour. Eating during class hours is disruptive under normal circumstances.
Atori's clearly leaning on the letter of the law for this goofy I-won't-tell-if-you-don't deal, but the basic principles behind "Students should be paying attention to their teacher during class and not distracting their fellow students with food smells and eating sounds/movements" are sound.
She's not the type be a disciplinary committee member because they would disapprove of her bring your puppygirl to school day idea. Yuu needs to raise the friendship level to see the full degree of stuff she's into that those prudes would be against.