A rational decision-maker using Bayes’ theorem would say, for example, that one should convict a black defendant with less evidence than one needs with a white defendant, because these days the base rates for violence among blacks is higher.

One would compare black defendants with guilty black defendants and white defendants with guilty white defendants. It's far from obvious that (guilty black defendants/black defendants) > (guilty white defendants/white defendants). Differing arrest rates, plea bargaining etc. would be factors.

Where do you think Pinker's analysis went wrong, if it did go wrong?

He began a sentence by characterizing what a member of a group "would say".