Interesting thread.
As myself, I have always loved the Hobbit and have recently grown to love Lord of the Rings as well. As a woman, none of these works seem very appealing. I know I risk some anger here, but the way Tolkien depicted women (if he depicted them at all) is not something I easily identify with. I don't think he really 'got' women, but which man really does?
Would female readers have been satisfied if Bilbo were Bilba? I highly doubt it. I just fail to see why the lack of female characters make this a 'boys story'. I'm not even quite sure what a boys story is. But the Hobbit is definitely not it. Any book which would be gender specific, should be gender specific. That is to say - how can you make a difference between boys and girls when this division is not even made in the book? The Hobbit is not about men and women. It is a children's story and children often don't really care about gender, unless the difference is enforced upon them by their surroundings.
I'm not explaining myself too well here, I'm afraid, but I think the Hobbit might be one of those stories that transgresses gender completely. Your female students obviously do not share my views, but I think that the Hobbit is neither about men nor women and gender is actually completely irrelevant in this book. As irrelevant as it is to young children.