Numo -- I think that your point is an important one. The equality of people in Zion IS an important aspect of the movie -- as one piece of evidence note that Cornel West, a leading authority on issuses of racism in America and professor of African American studies at Princeton, is one of the "actors" who plays a member of the Zion council. Someone like this would not have been asked to participate, and would not have agreed, if casting of minorities and the presence of strong female characters had been only a "movie gimmick".
It is indeed surprising that in Zion humans have managed to achieve so much more equality than is present in the matrix OR in our world -- it is human nature (one of the "grotesqueries"😉 for people to try to feel better about themselves by putting down other people/entities (including the machines), either on an individual or societal level. How did Zion manage to achieve this?
Your idea that people who do not accept the inherent inequality of the matrix/our world are more likely to reject the matrix is an interesting explanation -- only people with open minds get to Zion, leaving those predisposed to racism, sexism, "other grotesqueries", to exist in their pods.
In fact, one could say that the machines are helping the human race AND helping themselves by this selection process -- the subset of people of who end up in Zion are both less likely to kill each other, ensuring the future of the human race, AND to be more open minded to the machines, than the rest of the human race in the pods.
One could even imagine that this selection process was even one of the purposes of the subjugation of humans. I'm not arguing that it was the PRIMARY purpose, but it is a useful outcome that may be very intentional.
We will see how all this resolves (I guess) in the TMO civil war.. clearly there are still SOME people in Zion in whom "the grotesqueries of human nature" are still intact.