This moon imagery represents female reproduction, specifically here the menstrual cycle. The cycle begins once per month (controlled by the "flux" of the moon) and so is very much integrated into nature, an organic installment of life. However, this cycle is "eclipsed", literally overshadowed and suppressed "in these hips, / these loins", interrupting this natural cycle. These lines act as the final culmination of the transformation, the ultimate "unsexing" and dehumanization, as menstruation and live birth belong solely to mammals and are given special significance to humans as the utmost definition of physical womanhood. Without this ability, the woman becomes essentially a useless organism, and this is what Boland is attempting to convey. The social status of women is already one of such oppression that even removing the physical markers of femininity makes little difference to their status. Indeed, it would be easier to be a simple egglaying "sequin-skinned" fish than a woman who constantly strives for more than just maternity.
Interesting, here the word "loins" refers specifically to the woman as woman, as opposed to the swan-Zeus in Yeats' Leda and the Swan. Although in Boland's poem it is the woman who chooses her fate directly, in both cases it is the woman who must bear the burdens of her sex, both physically and emotionally.