One of the major issues that needs to be resolved in our lives arises when a duty we are called upon to undertake in service to the society or the social order comes into conflict with our internal sense of sin. This issue in fact became a major issue in the war crimes trials following the second world war and was eventually codified into international law that simply following orders that are abhorrent to the internal sense of right and wrong does not absolve one from the responsibility for the resultant actions. The modern interpretation is essentially that one must accept the personal responsibility to refrain even from a direct order if it is morally sinful or repugnant, and at whatever personal cost due to the power of the social order.
The underlying issues here were raised by Arjuna on the battlefield of Kurukshetra when he sought guidance from Sri Krishna. He recognized that it was his duty to conduct the war and overcome the opposing forces. He further was able to recognize that “right” was on his side in the conflict and that he was therefore justified by his duty and his obligations to the side he was supporting to carry this out. But he then recognized that the result would be the destruction of the social fabric, the killing of respected teachers and elders who were deserving of his love and respect, and who, out of a sense of their own commitments and duties, were obligated to fight on the opposing side. At this point, Arjuna saw the action as a sin, as something so repugnant that he could not obey the call of duty, and he declared that it was better to die unarmed and unresisting than to commit that sin.
The duty of society clearly objected to his view, but he was acting the role of the conscientious objector. The teaching of the Gita takes on this issue directly while proposing a solution that goes beyond the limits of either of the opposing principles.
Sri Aurobindo, Essays on the Gita, First Series, Chapter 4, The Core of the Teaching, pp. 30-31,
Sri Aurobindo Studies 