It sounds very wierd to me, but I think Scar is her father, first because of the green eyes, (I don't think the fur color mean anything, it doesn't has to be mixed light and dark, she probably has a color from either her mum or dad...) and if you look at it as the real world is, if someone else was her father, she would have been killed as cub. Lions don't want cubs that is someone else and then kill them, so, if Nala is still there, her father could for sure be Scar.
But it does sound very wierd (and this cousin thing doesn't matter either in that distance for animals or did I hear wrong about that earlier?), maybe we could just write to Disney and ask what they thought about it