You know, I hadn't even thought of gender playing into this. There's a line in the New York Times article about how the one of the producers thinks the theme of the books is "a little girl creating a new family", and pretty clearly that seems to be where he's going with the movies. I'm sure Lyra being a girl really didn't discourage anyone from doing so.

I feel like there's a real tendency in children's stories (and adult stories, really) lately to have the emphasis be on making a home or finding somewhere the character fits in, regardless of whether it's a story aimed at boys or girls. Stories that are about leaving a home and that experience are adult stories, always. Part of that, I think, is the perceived need for children's stories to have happy endings, which is much simpler with the first narrative. I wonder if some of the rest of it has to do with the current perception of the breakdown of the traditional family home and etc, and that many people no longer feel like they grew up somewhere safe and innocent (if they ever did, I guess), and so they seek that out instead of having to leave it.