This side of Heaven we will probably never know the man's whole story. At least we know his identity. I suspect Ford's 2nd Colo Cav and the company of 15th Kansas Cavalry and the others killed scores of those 81st and 82nd EMM, mostly when they caught up to them in the field. The reports in the "O.R." only state this generally because of the delicate nature of the subject. All Union troops literally hunted those guys down across that corner of Missouri for weeks, and some of them into Kansas and Nebraska Territory when they tried to escape from the death sentences that awaited them. The fact that they were fellow Union troops sealed their fate more than the "no quarter" rule already in effect on both sides in the guerrilla war. The southern nature of the "Paw Paw Militia" was widely known when that program began in fall of 1863 and heavily criticized, particularly in the press, so it was a big embarrassment when that many of them proved the naysayers to be right nine months later. Since you might say the killing was an "inside job" or "blue on blue," we will never know exactly how many were killed in all. The actual southern members of Thornton's command who were not EMM actually stood a better chance upon surrender of surviving past capture and to prison and to live beyond the war than did these militiamen who changed sides.
I need to interject, also, that large numbers of the 81st and 82nd EMM remained loyal, held to their oath, and performed their duty.