I think I've mentioned this elsewhere, but Persona 3 is a game about death, and how people react to death and loss. It's all over Persona 3's DNA. The original game's opening had "Memento Mori" and "Remember that you will die" all over it. Almost all the social links are all people reacting to death and loss in some way or another. One character loses their ability to walk. Another loses their aunt. One loses their brother. Another deals with the loss of their father and estrangement to their mother. Out of all of the Persona games, it takes its theme and runs with it to the very end in a way the other games in the series don't even dare approach. The Dark Hour is a literal metaphor for those who have experienced death or loss in some manner or way; those who can no longer regain that innocence back.
So what makes Aigis so unique here is that she is essentially a representation of the game's central theme of death as seen through the eyes of a non-human character who, none the less, is very much a living being. To summon a Persona is to be a living being; not necessarily to be human. But you are alive. You live, you experience emotions, you can feel just as any human does, even if not necessarily in the same way, and you can die. Hence Koromaru, Teddie, and Morgana as well. Aigis is very much a living being, and much of the story is here coming to the fact that she is not merely a weapon or tool to be used. She may be more durable than her teammates, but if her Plume of Dusk is destroyed, she will die the same as them. The more the story progresses, the more she starts to value herself in this regard. In this sense, she also gains "humanity", although not in the literal sense. However, with understanding what it means to live, she also understands that it means she can experience death and loss like anyone else. And that's what the end of the game is about - her experience with losing someone so important to her for the first time. Given that we have Episode Aigis/The Answer, it's no understatement to say she takes it poorly.
And this ties into another fact - Aigis is actually the YOUNGEST member of SEES. She may appear to be a teenager, but she is in-fact a year younger the Ken. When she's introduced, she's only nine years old, becoming ten years old as the story progresses. She also has a fraction of the life experiences and maturity that he has. For all intents and purposes, the other members of SEES are basically raising a young girl who just also happens to be a child soldier (THANKS KIRIJO GROUP) with access to ChatGPT for the entire game. So like many other children, it's not surprising she doesn't quite understand life and death as concepts at first, why it hits her so hard in the later parts of the game, and why she is so desperately trying to understand it during the later parts of the story. Because she's really way in over her head as a person, even if she's really good as an "anti-shadow weapon." The more the story goes on, the more she gets traumatized too, especially with all the plot twists too.
TLDR: The Kirijo group, sans Mitsuru and her father, are all monsters and Aigis is a precious little girl who should be protected at all costs. Unless you're fighting Shadows, in which case, let her do her thing.