Barbara,
I don't have a whole lot to tell you about the violence done against the Stokes in the Webster County area during the Civil War, but I give you what I can.

The Goodspeed series of couny histories was published in the 1880s, and the one you cite was published in 1889, so I have to look to what was available to the writer of the Webster County history to attempt to figure what he or she meant when they said "...a number of war murders, referred to in the military history..." Some of the Goodspeed county histories had a Civil War chapter pertinent to each county in that volume, but I don't think their history of Laclede, Camden, Dallas, Webster, Wright, Texas, Pulaski, Phelps, and Dent Counties had such a chapter. I could be wrong. If it did, then the author of the part about the Stokes men could simply be referring the reader back to the Webster County in the Civil War chapter. That could be what he or she referred to as "the military history."

If this particular Goodspeed county history did not have a specific Civil War chapter for Webster County, about the only thing I could think of would be that the writer MAY have been referring to the portions of US Department of War "Official Records of the Union and Confederate Armies in the War of the Rebellion" that had been published by 1889. I studied those seventeen or so volumes pertaining to the war in Missouri out of the set of 128 volumes, and I don't recall seeing any mention of violence against Stokes men by name, but I may have missed it or forgotten it over the years. That's about all I can contribute to try to decipher what the county history referred to in 1889 as "the military history." Other books and sources come to mind, but they all were published after 1889.

Regarding the Stokes men in particular, I obtained online records from the Missouri Secretary of State's Office about Granville Stokes' Union service as a private first in Company D, 6th Provisional Enrolled Missouri Militia between 19 October 1863 and 1 March 1864, which gave no other specifics.

I also obtained a copy of Corporal Granville Stokes' service card in Company M, 72nd Enrolled Missouri Militia between May 1864 and 15 November 1864 mostly in and from the county seat of Marshfield. Granville served a total of 52 days active duty in the 72nd EMM between 25 September and 15 November mostly at Marshfield. Corporal Stokes was probably guarding the company's rifle muskets at the county courthouse there, patrol duty, other guarding, details supporting the local Union provost marshal's office, perhaps duty at the nearby Union district headquarters at their large base in nearby Springfield. This was during Confederate Major General Sterling Price's great raid in Missouri during this period, and nearly all of the EMM were called to active duty, but, fortunately for Granville, Price's army did not come close to Webster County. Granville was probably mustered out of the 72nd in March 1865, when the program was dismantled to prepare Missouri to transition from martial law to civil law. Just as his service in the 6th Prov EMM mentioned above, there were no other specifics mentioned on his service card with the 72nd EMM.

You mentioned that William Henry Stokes joined a southern unit at Fulton County, Arkansas in the summmer of 1863. Joanne Chiles Eakins' "Missouri POW's" shows a military prison record for a Richard Stokes of Fulton County, AR who was captured by Union troops at Ironton, Iron County, on 27 September 1864. This Richard Stokes was probably one of the hundreds of wounded General Price's army had to leave behind after the Battle of Pilot Knob at that time. Union troops sent Richard Stokes to the military prison at Alton, IL and the remarks section says he was released from there 15 June 1865 when all the other military prisoners were released at the cessation of hostilities in this region. That's about all I could find on Stokes from around Webster County.

I am sorry I could not help more with your quest, and I wish you good hunting.
Bruce Nichols