Reconstruction was a war. The name "reconstruction" has an innocuous air about it. However, people were right to call it a continuation of the Civil War. It was also a largely unsuccessful effort at counterinsurgency.
As the Civil War Times article discusses, the Seventh Cavalry could not dislodge the Klan. Though the article gave the example of Major Lewis Merrill, his success seemed isolated. Those who came after him did not want to fight a counterinsurgency.
Militaries generally do not want to wage these kinds of war. They generally fight the wars that they want to engage in, not the ones they are fighting. This happened to us in Vietnam. We used tactics that were suitable for continental Europe and World War II. It's clear that our military learned from Reconstruction the same lesson it learned after Vietnam: it did not want to wage a counterinsurgency.
Militaries clearly do not want to engage in what they consider to be "constabulary work." The truth is that it is glorified police work. You have to gather informers, win over at least a segment of the local population and protect your people. The use of force has to be kept to a minimum. Militaries are not trained for this kind of work. They are meant to fight conventional wars with other armies.
There is also a danger when armies engage in counterinsurgency. They lose their ability to fight conventional wars. This happened to the Israel Defense Forces (IDF) in their war with Hizbullah in 2006. The IDF had fought the PLO and Hamas for years during the second intifada. The men in the ranks learned counterinsurgency tactics useful in the West Bank and Gaza but not in Lebanon. Many Israeli soldiers died when they used the tactics they had learned in the territories. As one Israeli said,"When you fight the weak, you become weak."
However, Reconstruction was a true forerunner of a 21st-century war. Like Israel's two wars against guerrila forces, the aftermath mattered as much as the fighting itself. The results of Reconstruction had as much impact as the result of the Civil War. The country was reunited but the blacks remained second-class citizens. As the narrator said in the documentary "The Civil War", "The South won that battle of attrition."