Mitsuru's Answer
In Persona 3 FES The Answer, Mitsuru never fully states what she believes to be the correct answer. Although everyone is fighting and stuck in the same day, she sides with Yukari. She sides with Yukari simply because Yukari supported her. Yukari wanted nothing more than to bring back M Protagonist, because she loved him (or at least felt very deeply for him) but she wasn't the only one. In fact, they all loved him (in the general sense of the word, not necessarily romantically). Without going into too much detail, there were four teams - those who supported protagonist's sacrifice, those who wished to undo it, those who thought they shouldn't be fighting each other, and those searching for their sense of self.
Mitsuru joins those who wish to undo the sacrifice so that m protagonist can be back in their lives. She knows it is a very selfish choice, but she makes the choice because that is what Yukari wanted. It was Yukari's choice and Mitsuru took it up as her own. Assuming that the player completes every social link the male protagonist can have dated Mitsuru or at the very least been very close with everyone. I believe, in part, that Mitsuru wanted the same thing that Yukari did. Not just counting if she and protagonist had been romantically involved. She drew strength from him and would have probably continued to so. I feel that if he had been able to stay, he would have been a very good sounding board for her.
I believe that even without Yukari stating they should be saving protagonist that Mitsuru would have reached that conclusion herself. One, she relied on him. And two, it would allow her to keep someone she cherished in her life.
By that point, Mitsuru has made many choices about SEES and her life. She is quick to appoint Aigis new field leader as soon as they realized she had the wild card. Mitsuru grew much more comfortable allowing the group to work and express themselves while playing an active part in helping to achieve their goals. I think it is only through her experiences with SEES and the support of the protagonist that she could genuinely allow someone else to have control. The wild card that Aigis had was familiar of protagonist and it would lead them to their goals.
Ultimately it is decided to leave protagonist where he is otherwise they will undo their victory. The dark hour would continue to plague them. I feel that it wasn't the end they wanted, but I believe it would also spur Mitsuru to find another way to help him. I think it would make Mitsuru appreciate protagonist all the more and give her a new goal for her future. I believe her answer would be to assist those who assisted her. Nothing more and nothing less. She helped Yukari and it would be simply time to help protagonist.