The higher criminality drives the police mistreatment. If you're a police offer and interact with mostly black criminals all day, your priors are set so that you think most blacks are criminals. So when you see an honest black person, you assume he's guilty of _something_, and consider framing him the honest thing, since you believe you're just putting the black man away for crimes he's doubtlessly committed, but for which you have no evidence.
(You should understand that _explaining_ something is different from _endorsing_ it. Of course we should judge people by their actions only. It is _understandable_, however, why the current police culture might have arisen.)