Spoiler for Half Knowledge:
I don't see Minamoto as a bad person out to cause trouble, but I think she can be a major factor in moving the story forward. That question she casually asked - "Oh, and do you like men?" has always been a sort of elephant in the room with this story.
In a sense - and this is symbolized by the uniform situation at the café - Nitorin has been living a sort of double life. He's avoided making the big decisions about his future (which is perfectly fine, as he still basically a child) but Minamoto might just be the sort of impetus he needs to ask himself the hard questions. He doesn't really know her - he can tell her things he'd be too embarrassed to tell his close friends or his sister.
It isn't just a "do you like men?" issue, and in fact Nitorin (unlike Mako-chan) has never expressed any romantic interest in boys, only girls. It's more of an issue of what kind of life he sees himself living as an adult, and of course Takako-sensei had to throw the cross-dressing Daddy in there at the end to really drive the point home...
