How can the American legal system which is so devoted to protecting individual rightsjustify itself morally if it jeopardizes, through its own...

It's an interesting claim being made.  I think it needs more detail and specific instances where this jeopardizing is happening.  I am not trying to speak from a zealot's point of view, but I think that the American legal system has one of the best self- corrective measures to ensure that it does not completely subvert the rights of the individual.  For example, the Constitution devotes much from the original 10 amendments to the rights of the accused and to provide a sense of institutional fairness and procedural due process to those accused of a crime.  While there is a jury trial system, there are also processes of appeals, judicial oversight, as well as other measures which can be theoretically enacted to ensure that individuals are afforded every possible opportunity to reflect their innocence under the law.  In terms of the law abiding citizen, here again, the Constitution speaks quite profoundly in guaranteeing a sphere in which individuals can be afforded a shield from excessive institutional encroachment.  The notion implicit in the First Amendment to be given a sphere of "negative liberty," the right to express oneself to be left alone, is something that every citizen possesses as an entitlement to not be harassed or molested from the external body.  Without a specific example, I can only point to the American legal system's theoretical notions that seek to protect the rights of all citizens.