You confuse different parts of the justice system, and your criticism is internally self-contradictory. If everyone who ever lived is guilty of something, then high or racially disparate incarceration rates need not catch innocent people. The fact that this occurs is more an indictment of the laws in place and the people who prosecute them, not the courts that adjudicate them.

Put another way, if breathing were a crime, then everyone convicted of it would in fact be guilty. If there were a lot of black men convicted of it, more so than other races, it would likely be due to different rates of prosecution, given how easy the charge would be to prove this is bad, but it is a criticism of the wrong part of the government. It would be like blaming the mayor for the ineffectiveness of the postal service (the former is the city government, the latter is federal).

Edited to clarify: I am referring to the value of our adversarial method and our rules of evidence / constitutional protections - the mechanics of how a trial works. There is an entirely separate issue of prosecutorial discretion and unequal police enforcement and overly draconian laws, which certainly lead to the problems being discussed here. But the entire purpose of evidence law and courtroom proceedings generally is to determine if the person charged is in fact guilty. It is not to determine if the prosecution is charging the right people or if the laws are just or justly enforced. So this criticism seems misplaced.