The way Haibara is framing the choice is similar to the choice Jo Walton explores in My Real Children, a novel about 2 timelines. http://www.jowaltonbooks.com/books/my-real-children/
The idea is that there are 2 worlds, one where the protagonist is personally miserable or less happy but their friends and the world are better. One where the protagonist is happier but the world is slightly worse.
I don't think it is a good framing or premise, and I have hope that the author of Haibara will go somewhere else with all this. There have been hints so far that this may be a false dichotomy.
Too often in stories, a person is asked to give up their magic or personal happiness in order for the world to thrive. Particularly female characters, but in this case a male character.
I am starting to find such stories tedious. I would rather talk about both/and stories than either/or stories.