I think a couple of the Alice books by Phyllis Reynolds Naylor address gay relationships, but I seem to recall that even though she was accepting and supportive, there was still something problematic about how she wrote about it. I can't remember exactly what bothered me. I've only read about 1/3 of the list, so it's possible I haven't read the books, and I may be confusing my concerns with some other series. Anyway, I can't make a whole-hearted recommendation and I'd suggest pre-reading or reading along with your dd if you find them. And I'm sorry, the list of Alice books is very long (20 or 30?) and I can't recall exactly which titles. Also, the series takes Alice from about age 7 through high school, each book dealing with "After-School Special Issues", so the later Alice books may not be appropriate for a 9 y.o. My recollection is that these books are set in Alice's middle school years.
Another Alice series, starting with Alice, I Think by Susan Juby, has a gay character - he's a friend of the family and kind of adopted uncle.
There is a gay couple in The Name of This Book is Secret by Pseudonymous Bosch.
In The Knife of Never Letting Go by Patrick Ness, the teen boy protagonist is raised by a gay couple and that is just presented in the background. It's not an "issue" to be dealt with in the plot. It's the first book in a dystopian trilogy meant for young adults and it's pretty dark, with some incredibly sad scenes. The second and third books are violent and disturbing. I don't think that it is what you are looking for now, but maybe in a few years...
Okay - I just re-read what I've written and it's not too helpful to you - sorry. I can think of some more good books like The Perks of Being a Wallflower and Will Grayson, Will Grayson, but they are all YA. I agree with you about the lack of depictions of non-traditional families for middle school readers.