My Rebel Ancestors??

I recently found in provost marshals papers a letter written on September 23, 1864, by Major J.B. Kaiser, commanding the Union post at Waynesville, Missouri, to Brigadier-General John McNeil, commanding the Rolla district, in which Kaiser identifies a number of citizens of Pulaski and Texas counties who had supposedly been aiding and harboring bushwhackers and "also conveying news to them by every opportunity they can get."
Among the people on the list accused of harboring bushwhackers was John Morgan, who was reported as living seven miles south of the Waynesville post. This was my great great grandmother's brother. In fact, the location Kaiser mentions, seven miles south of Waynesville is still the location of the Morgan farm, which has been in the family since about 1829, I believe.
Another person listed was the "Widow Tippet...where the Rebels make frequent visits for the purpose of gathering information." Mrs. Tippet was identified as living near Widow Adams, who lived west of Waynesville and was considered "a strong Rebel sympathizer." The Widow Tippet was John Morgan's sister and my great great grandmother. She had previously been married to my great great grandfather, Robert Wood. After Wood died, she remarried a man named Tippet, but he, too, died prior to the Civil War.
What I found particularly interesting was that I also found a letter written a few months earlier in April of 1864 by a prominent Union man named Ellis of Pulaski County to Colonel J.P. Sanderson, provost marshal general of the Department of the Missouri headquartered in St. Louis, in which Ellis identifies other men of Pulaski who can be trusted as honest and reliable Union men. One of the men Ellis mentioned was John Morgan.
This just goes to show how difficult it is for researchers to determine whether a Missouri ancestor (or any other person in Missouri) was actually loyal or not during the Civil War. Sometimes people were falsely reported as disloyal simply because a neighbor held a personal grudge against them, or else they were reported as disloyal on very scant evidence. On the other hand, sometimes people of suspect loyalty were reported as loyal because the person doing the reporting was of dubious loyalty himself. If Union authorities had a hard time knowing for sure who was loyal and who was not, how are researchers to know for sure 150 years later?
What I do know is that my great grandfather, Mrs. Tippet's son, joined the local Union militia near the tail end of the war when he was about 19 or 20 years old. Of course, by then many people who had previously nursed Southern sympathies had seen the writing on the wall and had shifted their loyalties, at least outwardly. I also know that two older sons of Mrs. Tippet, my great grandfather's brothers, were Confederate soldiers. So, as I say, the evidence is conflicting.