

Since Hannibal doesn't seem to love normal, but sees those he loves as an extension of himself, let alone the consumption angle and the mirror angle, instead of “normal” familial love, he might have developed possessiveness, territorialism and controlling, devoted protectiveness. 

He might aggressively protect her from external threats, bullies, or anyone he deems disrespectful, rude or a threat. 
An attack or insult directed at his little sister might be perceived as a direct attack on him and his authority. His retaliation against outsiders who cross her would often be disproportionately violent or vengeful.

Which brings us to the fear part. She might have a friend she had a fight with or a teacher who was unfair or something like this and this friend or teacher doesn't come to school/University the next morning. A few days later they are found dead and shown in a humiliating, artistic tableau. 

Mischa might share Hannibal’s olfactory senses and when he came back that night her nose caught a musty, rust-like scent (dried blood). If they share sharpness and intelligence, she might have found the recipes glued to the business cards. Or she might find the inspiration for the Tableaus (like Miriam found the ‘wound man'). 

But fear of losing her only anchor, fear of retaliation, fear of barely trusting anyone else, fear of not being believed (maybe doubt is also a side effect of Hannibal’s manipulation) leads to her not telling anyone, let alone confronting him. She stays away from other people and she becomes hyper vigilant around him, while also trying to be her old self. Maybe it helped that she was always more quiet than other children, especially after their parents died or after the prisoner had almost killed her.

Hannibal might try to control who she can hang out with, what she eats and how she spends her time. If she attempts to establish independence, he might respond with stillness on the outside and then gaslighting, or manipulation like he did with the replacements (Abigail/Chiyoh).

He might try to work to isolate her to ensure his influence remains absolute.
Hannibal might teach her how to lie, manipulate others, or break rules, celebrating her when she successfully pulls off a deceitful act, because he wants her to think, act, and view the world exactly as he does.

A betrayal (or perceived betrayal) might lead to emotional cruelty or sabotaging her relationships or a tantrum where he does something awful (like he did to Will in Mizumono).

Hannibal is highly aware of social expectations. Showing overt "love" or protectiveness over a younger sibling serves as excellent social cover, making it harder for others to accuse him of being malicious.

Mischa might feel safe under his wing while simultaneously feeling choked by his control (at least before she discovers the truth).

Over time, she might doubt her own judgement as her reality is constantly managed and defined by him. 

  
Will Graham: 

When she realizes Hannibal is obsessed and slowly falls for Will Graham, she might

a. Tell him to fucking run

b. If she trusts him she tells him the truth and can break free from Hannibal by working with Will

c. Gets jealous and the codependency Hannibal established make her sabotage the blooming relationship between the murder husbands

d. Dark armor/wingwoman: She makes herself invisible and encourages Hannibal to jump at the opportunity to finally break free from him and it's also an option that doesn't include prison or killing him. She also makes sure Will falls even harder and deeper for Hannibal.  

Unpopular opinion: Maybe alive Mischa would have been scared of Hannibal or would have suffered in his orbit...(Long text)