I think there are two distinct questions that you are co-mingling. The first is, do police only arrest (and prosecutors charge) people when they have strong evidence that they committed the crime? I think the answer is, "Yes, most of the time, in many districts" - but not all of the time, and not in all districts.
The second question is, "Should the court system act like the police only arrest guilty people"? And the answer is, absolutely not.
From your answer, I guess that you only cared about the second question. But the first question is the one raised by ProCicero, and is also an important question.
No the question of due process applies to who, how, and when the police decide to arrest people too. They should be expected to strongly apply due process and the presumption of innocence too. It's too easy to give police and prosecutors a pass on misbehavior if we characterize their primary responsibilities as focused on catching the criminals.
The second question is, "Should the court system act like the police only arrest guilty people"? And the answer is, absolutely not.
From your answer, I guess that you only cared about the second question. But the first question is the one raised by ProCicero, and is also an important question.