Well, History Buff....the border wars was a battle of farmers, farmer's sons and young men that had had enough of the Kansas Union units terrorizing Missouri. Kansas Senator, James Lane and his "Lane's Brigade" hit Osceola, Missouri and pretty much wiped it off of the map. When Quantrill hit Lawrence, the guerrillas were crying "Remember Osceola!"
Interestingly, Pro-Union Missouri Governor Hamilton Gamble also had to deal with the Kansans; the Missouri State Militia was organized as a local defense force to deal with Confederate irregular forces AND Kansas irregulars that were terrorizing Missourians.
Of course, not all the Missourians were not innocent; remember that "Bleeding Kansas" started partially due to "Border Ruffians" and "Pukes" crossing the border and illegally voting in KS Territorial elections in the 1850s. And then there was the Marias des Cynge Massacre just north of Ft. Scott, where Missourians rounded up a number of Free State settlers and shot them down in a ditch. And for that matter, The Centralia Massacre, where wounded Union soldiers were taken off a train, stripped naked and shot down in cold blood by guerillas.
As you stated, elements on both sides did bad things. Of course, the vast majority of soldiers, North & South, did not. I have an excellent article by John Bradbury which discusses soldier's letters from Midwesterners stationed in the Ozarks during the war. Like many American soldiers in a "foreign land", they are hardly endorsements for Ozarks tourism, but interestingly, many of these soldiers did return after the war, marry local girls, and settle down in the Ozarks.
Sorry for bringing this thread back -- I worked with the Civil War for 10 years on a daily basis.
T.