In principle, you are correct that superior orders are to be obeyed by a subordinate commander. But in the case of Johnston, I'm not quite sure whether the orders emanating from Davis did not leave a certain amount of wiggle room. Specifically, War Secretary Seddon instructing Johnston under Davis' authority on June 16, 1863 wrote, " Vicksburg must not be lost without a desperate struggle. The interest and honor of the Confederacy forbid it. I rely on you still to avert the loss." But in a further telegram to Johnston on June 21st, Seddon writes, "On every ground I have great deference for your superior knowledge of the position, your judgment, and military genius, but feel it right to share-if need by, to take-the responsibility, and leave you free to follow the most desperate course the occasion may demand." In other words, given the fact that Johnston had been given supreme command of the forces in Mississippi, Johnston believed he had a certain amount of discretion in carrying out the wishes of the War Department and the Davis government.