There is a notable wince of emotion before Naoto's detective sensibilities take over. As much as she doesn't necessarily want to be disloyal to her Senpai, she can see it. He is naturally lonely, someone who wants connections but before Inaba did not have many of them.

"It is, admittedly startling, however, I must admit, he does somewhat fit the profile of the sort of person who would do that. It is, in theory, possible that there is a world out there where I am the villain of the story."