Kirby,
As best as I can tell, Sisera and William were both living with their mother in 1860, and I suspect they were living on the property listed as S Threlkeld on the 1876 atlas. Certainly the property was large enough to "hide" a group of soldiers on. It also had the advantage of water, Richland Creek as well as the railroad and a road nearby. I do not know precisely where John was living in 1860, somewhere west of Givens and his mother and brothers, closer to Millersburg. The Threlkeld property is within a couple miles of Richland Church and 4 miles of Prairie Chapel Church.
So an alternative story may be John was on his way home, got caught, William and company happened along. Callaway county at the time seems to be a pretty closed community. Seems to me the Unionist all knew who the Southern supporters were and vice versa and seemed pretty content to get along until outside factions both Guerrilla and Union Militia started interfering in daily life.