It's because she isn't inspired by Aphrodite, she straight up is Aphrodite. In the original 1E sourcebook for the Realms, the Forgotten Realms Encyclopedia, Sune is mentioned as living on Olympus (what in later editions would be known as Arborea), where she is known as Athena. Given she's a love goddess, that's obviously a typo and Greenwood likely meant to say Aphrodite ("Sune" is even "Venus" spelled backwards with the V dropped), and Aphrodite was listed as CG in the original Deities & Demigods/Legends & Lore (and both 3E and 5E kept that alignment for her).