William S. Harney was one of those individuals who was genuinely horrified by the bloody St. Louis riot, which was a result direct of Lyon's actions in the Camp Jackson Affair. Now Lyon was subordinate to Harney, his actions were not authorized by Harney, but rather orchestrated by powerful Republican Frank P. Blair, who saw himself as the new commander of the Department of the West, and savior of Missouri, using Lyon as his primary tool. Harney no doubt knew the complex loyalties of the people in Missouri and wanted to keep the peace within the state.
The Missouri State Legislature responded quickly to the Camp Jackson debacle by reorganizing the militia as the Missouri State Guard, authorizing it to resist "invasion" by Federal troops. Harney, who saw himself as a treaty maker tried to calm the situation by a unique agreement, the Price - Harney Agreement (truce) with State Guard commander Gen. Sterling Price, who was married to Harney's wife's niece. The two agreed the MSG would control most of Missouri, while Federal troops stayed near St. Louis. This deal also involved the true Missouri villain, Missouri Governor Claiborne Fox Jackson. Jackson, who was a secessionist, agreed to swear allegiance to the Union. I have a lot of trouble believing this part as Jackson was only playing for time to build up the state guard. I am sure Jackson about choked on the words.
The Unionist leaders including Republican leader Frank Blair saw this as an unacceptable situation, since Price did little to nothing to prevent pro-Confederate forces from organizing across the state. He was also not interested in protecting any Unionists, who were still the majority in the state. Another factor in this sad state of affairs was Harney's Southern heritage, which brought his loyalty to the Union into question. Although born in Tennessee Harney was in truth nothing but an ardent Unionist. I am sure this played into Blair's hands when he reported this to the Lincoln administration in Washington, who authorized him to replace Harney with Lyon, which Blair did on May 30th. Lyon was not in charge long as Gen. John Fremont was appointed commander of the Department of the West on July 1st. Lyon had upset too many people in the state with his irregular war policies.
Harney was recalled to Washington to discuss the situation, but he was captured by Confederates while en route and offered a command by Confederate General Robert E. Lee. He turned down the offer, but because he was a Tennessean, and fellow Southerner, he was released and allowed to continue on to Washington. Harney remained in Washington and served in various administrative positions. Once it became clear to him that he would not receive an active command, he retired in 1863 and returned to live in St. Louis, Missouri. Blair and Lyon manipulated the situation to their advantage, but at the cost of turning Missouri into a very bloody battleground where paranoia and violence ruled until the war ended.
There is much more to the Harney story, but as this thread is about Lyon in Missouri, I will say no more. If someone wants to start a Harney thread they can, but most of his Army service was before the Civil War and controversial enough. He was seen as an honorable man before the war. He held the respect of many before and after the war. I think he was an old school gentleman, but a realist in war. One has to understand he began his Army career in 1818 under Andrew Jackson.