The intellectual tools to defuse the danger are available. "Is" does not imply "ought. " Group differences, when they exist, pertain to the average or variance of a statistical distribution, rather than to individual men and women. Political equality is a commitment to universal human rights, and to policies that treat people as individuals rather than representatives of groups; it is not an empirical claim that all groups are indistinguishable. Yet many commentators seem unwilling to grasp these points, to say nothing of the wider world community.
Well, I think that it would be first good to establish if it is a genetic trait that people tend to think of others in terms of group stereotypes. That wil determine if any intellectual tools will really be effective.
Also, pursuing Pinker's hypothesis, presumably some groups are more genetically prone than others to treat people not as individuals but rather as representatives of groups. It would be extremely strange if just this aspect of temperament were entirely learned and had no genetic component. It would be worth researching this as well, and using some of those aforementioned intellectual tools to figure out how to handle this. We find it hard enough to treat people as individuals rather than bearers of particular skin colors. How much harder to handle as individuals the hypothetical group of people that are genetically pre-disposed to bigotry!