Think of it this way...Many pagan religions have main Gods/Goddesses and with those come sub-gods/goddesses. I wouldn't doubt that Hyrule has the same idea. Of course we don't know too much about their religion to say so, but it would only make sense. So, in accordance to Skyward Sword we know that there is ONE main Goddess so far, as in the trailers and in the gameplay videos we see Ghirahim talking about "the goddess".
So I think of it this way. Goddess (unnamed) > Din, Nayru, Farore > Goddess of Sand, Goddess of Time. To make this clearer, think of Ancient Greek Mythology where at first you had the Titans that were the main deities before the Olympian Gods/Goddesses came to be. When the Great War commenced, the Olympians usurped the Titans, thus becoming the main gods/goddesses of Ancient Greece. So then now we have the 12 MAIN Gods/Goddesses that comprise of Zeus, Hera, Poseidon, Demeter, Athena, Dionysus, Apollo, Artemis, Ares, Aphrodite, Hephaestus and Hermes. In accordance to this, there are sub gods of Greek Mythology. There are many so i'll just name some: Aeolus, Harmonia, Deimos etc, etc.
So I wouldn't doubt that the Hylians have a religion similar to Greek Mythology, where they know of minor goddesses but really only praise Din, Nayru, and Farore. Also think of Judaism, Catholicism and Islam where people worship ONE central God, but have major/minor prophets or deities. Examples of this are Moses, Jesus, and Mohammed. All in the all, the Goddess of Time could very well be a minor goddess
I hope this helped.