> The prosecutor can refuse to prosecute a guilty party.
But this is intended as one of the checks and balances. If the legislature passes an unjust law or one with unjust applications, the prosecutor can exercise their discretion and not enforce it, acting as a check on the tyranny of the majority.
You could remove prosecutorial discretion and require prosecutors to proceed against anyone someone wants to file charges against (let the judge and jury sort it out), but now you're making a trade off against something else.
Notice that this applies to any of the rest of it. Congress could refuse to pass a law that makes sense because their cronies benefit from the status quo etc. But the concern here is that the government has an unprecedented capacity to do harm because it exercises a monopoly on violence. If the prosecutor's buddy is a serial killer, you can still exercise your right to self-defense, or avoid being alone in public. If the prosecutor's buddy is allowing your company to not pay you for hours worked, you can sue them yourself, or quit. All while lobbying the government to replace the prosecutor. If you're falsely imprisoned by the government, what are you supposed to do?