Harry and Ginny doesn't work in the books though either so what can they do? Ginny isn't written in much depth so whats Bonnie meant to do with her? Indeed, as Hermione is avoiding the obvious too, what else is Emma to do with Hermione except add a few layers of armour?
The whole thing is written to artificially avoid Harry and Hermione ending up together so is not surprising if it doesn't work completely. Its also got to set up Hermione and Harry's closeness (they are the unbreakable bond) for the next two films which would look odd too if Ginny/Harry was more central to this film.