Should we define minorities in terms of gender as well as race and ethnicity?
I think that the answer to this is a function of our purpose in so defining and also a function of what is meant by "we." As a general matter, I would say that if our purpose is in protecting minorities from discrimination and if "we" are the law and society, then we should define females as minorities. I would add the caveat that we are coming to understand that "gender" is a far more complex concept than we knew heretofore.
The term "minority" is not the best term to use in this discussion, since there are so many instances in which a numerical majority is being discriminated against. For example, in the South, before the Civil War, I would guess there were many places in which African-Americans were the majority of the population. And certainly, there are places where females are in the majority. In neither example did or does the group's numbers protect against any number of forms of discrimination.
In the law, the reference is always to "protected class." These are classes of people we have chosen to protect against discrimination, and gender has been a protected class since the Civil Rights Act of 1964, as have been race, color, and ethnicity, in the form of ancestry or national origin.
Now, if our purpose, that is, the purpose of law and society, is to protect people from discrimination on the basis of their gender and the term "minority" is used to signify this, then I think we should continue to use this definition, as we have for over fifty years now. This is an acknowledgement that males and females can be and are treated differently, in any number of different contexts. The glass ceiling persists, women are often discriminated against in male-dominated environments, and men are often discriminated against in female-dominated environments. There is nothing to suggest that these problems have gone away, just as there is nothing to suggest we are living in a post-racial or post-ethnic world.
Having said all of that, there is a general consensus that "gender" is a social construct, that "sex" is a biological construct, and that neither is as clearly defined as we once thought. We are coming to understand, for instance, that people are sometimes born in a biological state that is completely incompatible with what they feel is should be their sex, or with attributes of both sexes, and that even chromosome testing is not completely definitive. We have people who are male and who live as females and females who live as males. This is not nearly as binary as we once believed.
Nevertheless, given the purpose of defining gender as "minority" to be to protect people from discrimination on the basis of gender, the complexity of gender and sex should not really matter at all. The whole point to law and society labeling a group as a minority is to acknowledge that a group is treated as "the other" by society, and that this group is in need of protection. The law and society cannot eradicate prejudice, but we can discourage discrimination by this means.