I think you raise an interesting point about the use of color in Maguire's novel Wicked: The Life and Times of the Wicked Witch of the West. I always am drawn to the use of color in texts and this novel's use of color definitely drew may attention.
While I think that you could be right about the use of color referring to racial identity (and, therefore, racial prejudices), I have also examined the possibility that it refers to the simple idea of good and evil (which I suppose could be aligned with the racial lines as well). One could support this based upon the fact how the characters in the novel are perceived by others simply regarding the color of their skin.
The curious part of the novel is its underlying themes regarding religious ideology (which could be depicted by the different associations of color) and the power of woman. Given that the novel depicts both "good" women and "bad" women, one could suggest that the use of color more specifically speaks to the plight of women within their own social circles (women of different color).
The wonderful thing about literature is the fact that all texts are simply open to interpretation. I would be curious to know if others in your reading group see color in the same way you did/do.