“How can a progressive, important intellectual community behave so poorly towards its female peers?”
Because atheism’s fundamental intellectual commitments (if pursued consistently) lead inexorably to such behaviour.
This article (not for kids to read, by the way!) shows the fundamental incoherence and hopelessness of atheism, because it displays the logical devaluation of the individual that inevitably results from naturalistic materialism. See, if human beings are merely animals and there is no transcendent, objective morality, “might makes right”–and men, being stronger than women, dominate in the jungle of naturalistic materialism. On atheistic grounds, how would that be wrong? (How is there any right and wrong to begin with, anyway?) If evolutionary theory is right, men increase their chances of reproductive success by objectifying women, using them as means to an end rather than valuing them as individuals.
But, if there’s a God and he made gender and sexuality for a purpose–and if men and women are made in his image and derive their value from him–then, and ONLY then, we have a basis for the inherent equality of men and women. The answer to this behaviour, then, is the Gospel.