How can the American legal system devoted to protecting individual right justify itself morally if it jeopardizes the right of law abiding citize?
It would be helpful if I knew exactly why you feel that individual rights of "law abiding citizens" are being infringed upon. In certain situations though you are probably correct.The American legal system is by no means perfect or without fault. That being said, I think that the majority of the time we do a good job in protecting those same civil rights.
Along these same lines, an argument could be made in regards to entitlements and affirmative action plans. Some authors argue that these plans are "reverse discrimination". In these cases, the rights of whom are being trampled upon? The answer lies in to whom you ask the question.
I think that more specific details or situations would be needed in order to fully answer the question. In the broadest of senses, the question does pose where the fundamental challenge of any rights based system. On one hand, there is a desire to protect the rights of every individual. Yet, there are moments when the protection of one's rights detracts from the full expression of another's. There is a balancing act that must be struck existing between the protection of the rights of the accused and the rights of the law abiding citizen. In the end, this valence is not a static one. It is dynamic and fluctuates with each decision in our political order. One can hope that there is balance and that the rights and advocates present speak out when they sense that individual liberties are threatened, but this balance is what defines political orders predicated upon the preservation of rights and individual entitlements.
In order to answer a question like this, we would need to know exactly how you are saying that the US legal system jeopardizes the rights of law abiding citizens. This is just sort of a blanket statment -- the system jeopardizes rights -- without any specific allegation that can be addressed.
Typically, a legal system can go wrong because it is hard to balance the need to protect the rights of all people (the accused and the law-abiding alike). It is also hard to balance the need to keep order and safety and the need to avoid abusing people's rights (the order vs. freedom argument). But without a specific case, I cannot really say more than this.
There major consideration for justifying the legal systems that seems to violate individual rights is the issue of identification of limits of individual rights. No society can or does provide unlimited individual rights of any kind unmindful of the impact of such rights on other individuals and the society as a whole. The society gives the individual the benefit of cooperation which they cannot obtain with their individual efforts. However, cooperation also involves individual giving some of their independence for reaping the benefit provided by society. If individuals, because of criminal tendencies, or some misguided concepts about need for unrestrained individual rights, fail to voluntarilyy submit to the necessary restraint on individual rights essential for smooth functioning of the society, and yet expect to continue to enjoy all the benefits provided by the society, then society is definitely morally justified in enforcing by law discipline among such individuals.