I skimmed the study months ago, and while you're right that Fryer performed a deeper study into use of force in Houston, the results from the 10 cities are roughly consistent. As the article states, across the ten cities, officers were more likely to fire their weapons without having first been attacked when the suspects were white. I have no issue with people criticizing police for use of force, but this isn't a racial issue.
Regarding your second point, I think you're mistakenly conflating inequality with inequity. Without looking at any specific data, I wouldn't doubt that blacks experience a disproportionate number of encounters with police compared to whites (or other races). That's inequality. But the data does state that blacks also commit a disproportionate number of crimes compared to whites. Black men between the ages of 18 - 34 comprise about 4% of the US population and yet commit about half the murders. As a result, it's understandable that blacks experience more encounters with police than whites. Inequality of encounters isn't necessarily indicative of inequity or racial bias.
In a similar vein, men comprise about 49% of the US population and yet they comprise 90% of the US prison population. I don't think that disparity is the result of a sexist justice system, just that men tend to commit more crimes.