I'm no expert at all, but i did do a little research about this. I came up with a few from a little encyclopedia i was looking in. It had basic themes the gods were about and little categories, which is how i complied the list.
The list i kinda found: Artemis, Athena, Awashima, Bahuchara, Erinle, Ezili Dantor, Hyacinth, Kybele, Longunede, Narcissus, Ochiossi, Oshumare, Pan, Triana - and also Archangel Michael?
Now, a lot of these God/desses are either loving, for women, or stand for something of the sort. Some are just all accepting and some i haven't ever heard of. But it is a list! Note that i haven't done much research into these gods because of personal issues taking up residence in my head. Hopefully it'll help someone though!
Also, just because I wanna put it in here too: Loki <3 Everyone cites Loki, though the book i was reading was rather cruel towards him and didn't mention his love for genderqueer individuals at all! *harumph* I followed him for a long while, and he's still close to my heart. But he is not for everyone, i can say that. x.x