The Moral Legitimacy of Refusing to Fight in an Illegitimate War
Upon the realization that their primary function is to wage war and kill other human beings, some soldiers , pursuant to the dictates of their consciences, refuse to fight and apply for discharge from military service as a Conscientious Objector. That is, following a religious and/or moral "awakening," the soldier determines that war is either always morally wrong and a violation of conscience - General Conscientious Objection (GCO) - or, if not always wrong, it is wrong and a violation of conscience in the particular circumstance in which the soldier is required to fight and kill - Selective Conscientious Objection (SCO). Conscientious Objector (CO) status may be granted, however, only to soldiers who are able to demonstrate a "firm, fixed and sincere objection to participation in war in any form or the bearing of arms,"  based upon "religious training and belief," to include strong moral and ethical convictions, that has "crystallized" since enlisting in the military. Consequently, Selective Conscientious Objectors are not eligible for CO status.
This distinction between General and Selective Conscientious Objection and the military's refusal to acknowledge the latter presents the soldier with a crisis of conscience regarding whether to follow orders and participate in what he determines to be an immoral and illegal war or to follow the dictates of his conscience, disobey orders, refuse to fight and face serious disciplinary action. Upon analysis, it is clear that the military's position on CO status is morally and legally untenable - inconsistent with the demands both of morality and of law.
Inalienable Human Rights and Conscientious Objection
Religion and the rule of law teach us that life is sacred and inviolable That is, that human beings possess an inalienable right to life. Correlative to this right is the moral and legal obligation not to kill another human being, i.e., not to violate this right in others. This inalienable right to life is the basis of the Just War principle that requires innocents to be discriminated and afforded immunity, that they not be attacked, injured or killed in war. In the view of the GCO, this right and immunity can never be overridden or forfeited. Hence, war is never a moral option. For others, however, rights are not absolute, but prima facie. That is, under some conditions, rights and immunity can be forfeited, rendering the individual liable to be justifiably injured and/or killed in war. Hence, some wars, wars against aggression for example, may be morally justifiable and provoke no objection of conscience even should the use of deadly force be required. What soldiers with either perspective have in common is the conviction that should they be required to participate in an illegal and immoral war and to kill innocents, given the sanctity and inviolability of human life, they have a moral obligation to refuse to fight, an obligation to become a CO.
The Legal Concern
Military theorists, at least sincere and knowledgeable ones, realize that wars can be just or unjust. Further, they understand that, despite being subjected to rather sophisticated Pavlovian conditioning techniques during basic training intended to prepare soldiers for battle and to overcome what Gen. S.L.A. Marshall identified as an aversion to kill, soldiers must maintain an ability to make moral and legal judgments. That is, the military does not want robots, programmed automata that respond unquestioningly to superior orders. By law, soldiers are not required to obey all orders.
"The fact that a person acted pursuant to order of his Government or of a superior does not relieve him from responsibility under international law, provided a moral choice was in fact possible to him." 
In fact, at least since the United States Nuremberg Military Tribunals (NMT), soldiers are legally obligated to sometimes disobey superior orders. US chief prosecutor Robert K. Jackson at the NMT declared in 1948:
"[T]he very essence of the [Nuremberg] Charter is that individuals have intentional duties which transcend the national obligations of obedience imposed by the individual state." 
United States Uniform Code of Military Justice (UCMJ) 809.ART.90 (20) makes it clear as well that a soldier is required only to obey the "lawful command of his superior officer." The obvious implication of this is that military personnel should, in fact they are required, under threat of legal sanction, to disobey an unlawful command or order. Clearly, then, under International and US Military Law, the individual soldier is empowered to make critical legal judgments, many times under very stressful and coercive conditions, regarding whether to obey or disobey an order.
The Order to Fight in an Unjust War Is an Illegal Order
To wage an unjust war is a crime of aggression. Aggressors, because they violate the rights and immunity of their victims, are acting illegally and immorally. They are Unjustifiable Combatants. Consequently, Unjustifiable Combatants suffer the sanction of forfeiture of their rights and immunity and become liable to be harmed and killed, all things being equal, in self and national defense. The victims of aggression, however, have done nothing to warrant forfeiture of their rights and immunity. They are innocent and maintain their right, their privilege, to war against the aggressor in self and national defense. They are Justifiable Combatants. In war, then, all combatants are not moral or legal equals.
The order to participate in a war of aggression and to kill innocents (Justifiable Combatants or noncombatants) violates the sanctity and inviolability of human life and the tenets of international and United States military law. Consequently, the order to fight an unjust war is an immoral and illegal order and an affront to conscience. Because leaders may be incompetent or corrupt, and because human beings remain responsible for their actions despite becoming members of the military, soldiers must not unquestioningly obey orders and presume the war to be just. Rather, before participating in war, they are morally and legally required to make the important, though oftentimes difficult judgment regarding whether the "enemy" maintains or forfeits his immunity, i.e., whether the war is just or unjust. Further, should their determination be that it is unjust, not only can soldiers refuse an order to fight, they are legally and morally obligated to do so. That is, they are legally and morally required to become Selective Conscientious Objectors.
A False Distinction
Inalienable human rights are values we hold sacred in this nation. In granting CO status, the military is recognizing and accepting the validity of these values and indicating a respect for the religious belief and/or moral imperative of soldiers to act in accordance with the dictates of conscience pursuant to these rights, i.e., to refuse to kill innocent human beings. Theoretical ethical variations in the scope of application of this right, whether the soldier accepts rights and immunity as absolute - killing is always immoral (GCO) - or prima facie - killing is sometimes permissible (SCO) - while, perhaps, of interest to ethicists and philosophers, should have no relevance to determinations of CO status since in either case; morality and law demands that soldiers respect the rights and immunity of innocent human beings and refuse to kill.
Consequently, there is no moral or legal basis for the military to distinguish between GCO and SCO, accepting the former and rejecting the later. This is particularly important in a society that, while not condemning all war, does recognize the very real possibility that some war may be immoral and unjust. Finally, the failure to recognize SCO is inconsistent with the accepted legal obligations of soldiers as established by the Nuremberg Principles and the Uniform Code of Military Justice to obey only legal orders.
Whenever a soldier refuses to obey an order to fight in what he deems an immoral war by virtue of a decision of conscience, it is not only appropriate, but morally and legally required to "put the war on trial" as well. While it may be the case, that individual determinations regarding the morality and legality of a war may be mistaken, since national leaders make mistakes as well, the soldier's decision of conscience must be taken seriously and given credence through a fair and legitimate hearing or trial that does not accept the war's justness as given. Consequently, such proceedings must go well beyond the two questions that have typified courts marshals to date: "Were you given a command to fight in Iraq?" "Did you obey this command?" and must include a third and most important and relevant question, "Is the Iraq War just?"
I have argued that the act of fighting in an unjust war is illegal and immoral. I caution the reader, however, to avoid repeating the mistakes of the past (a mistake, I fear, that is again gaining acceptance among a frustrated activist community) of moving from the illegality of the war to the criminality of the warriors. There is a profound moral and legal difference between condemning the act and blaming the actor. Determining moral and legal culpability is a complex process that goes well beyond a determination that the war is unjust. It must involve as well an evaluation of individual motivation, intention, whether the soldier has the information necessary to make such profound moral judgments, and, as stated in the Nuremberg Principles, whether "... a moral choice was in fact possible to him." While we admire and praise those who are capable of making such judgments and possess the moral courage to act in accordance with the dictates of their consciences, given the severity of the legal and social sanctions the soldier must suffer, it is not at all certain whether refusing to fight under the threat of such sanctions is obligatory or supererogatory - "above and beyond" what we can morally require a person to do. What is even less warranted is to blame the warrior for the war as though his not refusing to fight is the cause and the reason the war continues. Rather, we must understand that ultimately the responsibility and blame is with those who manipulate, deceive and use war as a means of acquiring wealth or power. We must understand that in a democracy all citizens bear responsibility for the actions of their government, and that there is blood on all our hands. We must understand that rather than to condemn and vilify the soldiers, we must educate and help them comprehend the true moral and legal nature of war. Most importantly, we must strive to create an environment in which adolescents and young adults feel empowered to act upon their moral convictions and refuse to fight. Finally, we must ensure that refusers and deserters are supported and provided protection either through SCO laws, legal defense funds, or, more drastically, by providing sanctuaries from military apprehension and prosecution.
 For purposes of convenience, I will use the generic term "soldier" to refer to all members of the military regardless of branch of service or gender.