Well, it's not just a conflation. Many police departments that deal with those types of inner cities are either taught or learn from peers or experience with peers to view things through a racial lens. If police take the viewpoint that they are "at war" with criminals (which is a huge viewpoint in the inner city among police), and most of the criminals are a certain race, then they will have the same problems as soldiers, in which some just relate the race/ethnicity of the country in which they're fighting as the enemy and gradually dehumanize them (including civilians), or view them as "others" in their own minds, which causes them to treat them differently. You're dealing with natural human things like selection biases and snap judgments, that are dangerous when the people doing so are often armed, and can get away with much more than a normal citizen due to being more protected in various ways (by other police, by prosecutors who depend on police for convictions and don't want to get on their bad sides, etc.).
That's the "racism" that is talked about in that context - a large portion of people that harbor an automatic snap shift in how they view black/latin/whatever people due to working in areas where those people are the underclass, and thus, more likely to be criminals. It doesn't mean a default hatred, it's a difference in how one approaches or treats someone based on race, including assumptions of criminality or danger. Even if it's UNDERSTANDABLE, that does not make it RIGHT for those that are victims of it.
However, since police departments are institutions, something can be done DIRECTLY about this. Better training, forcing at least some education about basic socioeconomic theories to police, better oversight, not letting prosecutors with conflicting interests handle grand juries in those types of cases, not letting people with obvious psychological issues carry guns around as an arm of the state, etc. That's the kind of change that can be forced if enough of the populace turns against it.