This poem actually makes a number of profound statements about gender relations and also art and the depiction of women. However, you are right in identifying the gender inequality between men and women to be a key theme of this exciting and memorable poem. Key to understanding what Christina Rossetti is trying to say through this poem is the way that the woman, who is obviously the muse of the unnamed male artist, is used and abused by the painter. Note that it is "one face" that dominates all of his work, "one selfsame figure" that is depicted in a variety of different guises, whether as a "saint" or as an "angel." However, as the last few lines of the poem make rampantly clear, that all of these paintings do not show this woman in her reality, but only how she fulfils the fantasy of the artist:

Not as she is, but as she fulfils his dream.

The meaning is evident: women are not entitled to their own identity and existence. Rather, they are dependent on men to be given that identity and stereotyped reality that is really no reality at all. In a sense, we could argue that the artist/muse relationship is an allegory for the role of women in Victorian society. They only have license and independence in as much as they "fulfil the dream" of the patriarchal society in which they live, that is able to cast them in what role they wish, but always denies their own independence and reality. Women are shown only to be viewed through the male gaze that objectifies them and disempowers them.