No doubt bad or corrupt COIN personnel are a real problem in that they push people to the other side. I have done a fair amount of reading on Missouri and with a gun to my head I have no idea how many guerrillas their were in Missouri. By listing all the Union COIN regiments maybe we can make a reasonable guess.
I know there were a lot of COIN units in my part of Missouri alone, and counterinsurgency took a lot of time and manpower. I was just reading the reports leading up to and after the Centralia Massacre. Even before the Massacre, the Union commanders were throwing a lot at Anderson, and they almost had him at Huntsville two days before. If he had just lingered a little longer he would have been caught between a dedicated COIN unit and the militia in town and the 9th Cav MSM that just happened to be in town at the time. It would have been a bloody mess, and a major battle for this area, but the Massacre probably would not have happened. But just reading the reports you get the idea there were only two types of units in Central Missouri. First there were the local garrisons like the 46th EMM, and then there were the MSM which seemed to be dedicated COIN units. That is a bit of an exaggeration as you did have regular army units also, but they were being use for counterinsurgency too.