Thank you for that detailed, sad story about what happened to your husband's ancestor. I would say from some of the insight that you revealed that you seem to have an accurate assessment of "how things were" in Missouri during the way. At least you know more than many descendants about why great, great grandfather failed to come home from the war.
I looked up William Keith and Thomas Clark in the MO Sec'y of State's website's online military service record and found two privates by those names who served most of 1863 on active duty in Company B, 1st Regiment Provisional Enrolled Missouri Militia. They were normally assigned to the militia company at Danville, west Montgomery County. I wonder if they were picked to go in disguise to test the loyalty of Callaway County farmers since they were probably not known outside of Montgomery County.
Yes, Joe Cole and the brothers Frank and Barton Ramsey were "particulary 'bad guys'." Something I had published earlier this year describes some of their escapades in this region during the year 1863, also mentions John Day's spectacular escape attempt from Gratiot Street Prison. During 1863 I imagine people for several counties around knew about these Joe Cole and the Ramseys. Cole was killed before the year was out. I will be writing more about the Ramseys in my next work now in progress.
The death lists from the St. Louis military prison hospitals were issued just about daily in the St. Louis newspapers. Bear in mind that all the article will mention inside a list of men who died that day is your man's name and perhaps county of residence and little else if anything. Outlying county newspapers would read those lists and republish in their weekly papers names of men from their county. It wasn't an obituary, but at least it got a mention so the family and neighbors would know. I have seen very few obituaries in the MO wartime papers. I wonder if that practice began after the war.