Actually, I don't see Ravenclaw as Hermione's secondary house at all - I see her as more of a secondary Slytherin (she views knowledge as much more of POWER/a means to an end if you ask me)! And placing Hermione in the dungeons would either prevent the trio from ever forming (leave that Slytherin to die) or give Harry a completely different attitude of Slytherins by the end of year one...

William//Slytherin