As far as what was shown, Hanabi just treats the protagonist as just another one of her guy friends. Or at least, it wasn't shown whether she is closer to the Kimimaro anymore than any of the other guy friends (ex. everyone else calls her Hanabi as well).
That's why I don't see how Hanabi getting a boyfriend is NTR in the slightest. NTR is suppose to rouse jealousy (or as I like to more specifically put it, "I want to punch someone in the face" feelings
) because the protagonist had someone precious 'stolen' from him. And for someone to be 'stolen' from the protagonist, the story must have established early on that the two were close and the girl must have slowly drifted apart.
This show on the otherhand pretty much establishes from the get go that the two aren't any more than friends, and yet the two haven't drifted apart as friends either. If anything, the protagonists feelings seems more like its been unrequited for quite some time, and that is the farthest thing from being NTR from what I understand of the term.