Mitsuru's Struggle
For me, Mitsuru's struggle has always been about her devotion to those she loved. She has to balance her duty to her family and her friendships with SEES. She has the latter only because of the former and I think she knows that. She is slowly cleaning up the mess her family made but at the cost of trust with others. She knows that when she keeps things to herself that she is not cultivating friendships, but initially she's not trying to do that. Her goal is to stop the Dark Hour that her family created. On the other hand as she starts to trust SEES more she sees just how much trouble she has caused people. She's no longer the model student or the ideal because she was part of something so terrible. I think this eats away at her knowing that every person she's connected with is simply a bystander or byproduct of her family's stupidity. She can't fathom whether or not she's doing the right thing bringing in others to assist her or if she should go it alone. I think if she could have handled it alone, she would have. If there was no real need to involve others, she wouldn't have. She is then faced with a shortcoming in the idea that as much as she wants to be the one to clean up the Kirijo name and strife, she can't. Not by herself at least, and she falls short of perfection that she has longed for.
As we know, Mitsuru gains her persona to protect her father. Her father is the reason she did many of the things she did and the reason for the choices she continues to make. She wants to do well by him and make the Kirijo family a respectable name once more. She bears this cross! She takes up this cause simply because it was her family who did it! I feel that she keeps people at arm's length because of that. If people knew, would they still want to be around her?
When confronted with Yukari's distrust, we can see the guilt on Mitsuru's face and hear it in her voice. She didn't want to keep things from SEES. She did it because she felt it was the best option. She had justified the idea as being a trust one. In which SEES most likely wouldn't trust her if they knew that her family had created the issue at hand. Unfortunately, her withholding the information causes more tension between her and the group. Mitsuru wants desperately to trust them but I can see how it would be hard for her knowing that her own family created the problem. Thus making trust extremely fragile to her. After all, her family was her reason for living but they committed such a grave and terrible act! Their actions caused the deaths of many and would continue to cause problems for people a decade later.
With this in mind, I believe that Mitsuru used SEES as a way to remove the stain on her family's name but I do not feel that she was being malicious. I think that she used her resources to the best of her ability but is unskilled in speaking on more personal and intimate terms with people. Her inarticulation causes her even more problems as when faced with a crisis she cannot describe how she is feeling or what should be done. This causes her problems to grow even larger.
After everyone finds out about Kirijo, though, I feel that they don't specifically blame Mitsuru so much as the company. However, she takes it to heart and it weighs on her. What can she do to make it better? I think that's all she's ever been about. Redeeming the mistakes of the past. At least in terms of trust, she takes on everything herself often relying on the only person she really can. After all her motives are genuine enough and she knows (more or less) what she wants. She can't say that for other people and this is probably one reason she keeps her thoughts to herself and keeps people at arm's lengths. She has been raised to be cautious.
Another thing to consider is that Mitsuru has had a very strict upbringing. She admits to having little fashion sense because other people pick out her clothes (so she's always fashionable). And she often reminds herself that there are things she can do (or wear) and things she cannot (even if she wanted too). She envies Yukari a little for this but it never reflects badly in the way that she treats her. Mitsuru has been raised to be a very specific way, most likely because Kirijo Group caused a lot of problems. I do not believe that her father was harsh, necessarily, but I do believe that he controlled many aspects of the way she lived. She was raised to be independent and conscious of her actions. She knows she is a role model and she should always be the ideal to strive for. That kind of life would be very dull and tedious as she lacks freedoms that others her age have. I believe this makes it hard for her to relate to her peers which in turn makes it difficult for her to make friends.
At the end, she rides a very fine line between friendship and duty, often choosing duty because it is all she's ever known. As she makes more friends she begins to open up and reconsider what would most beneficial for Kirijo and herself. But it is not without doing things she would not normally think of. She still doesn't stand up for herself but she is much more adamant about defending her friends. I can just see her stressed out at the end of the day trying to figure out where she went wrong for someone else to insult someone she loved or cherished. Mitsuru takes things very personally and internalizes them, only lashing out when someone else is hurt (or could be).