I just found Col Thornton's military record incorrectly listed on the 1890 Union Veterans Schedule. His line along with Confederate soldier's record is lined out and x'd out.
It's at ancestry.com, easy to find searching Thornton, John.

Entry shows: House 265, Family 267, Louisa A, widow of Thornton, John C (Conf), Recruiting Officer, Gates Regiment, Missouri, Enlisted Oct 1861, Discharged 1865.
Home: Butte, Silver Bow, Montana.

His wife tried to get his name included, I wonder if she knew what a monster he really was.

In 1880, he is living with his wife and 8 children in Butte. In 1850, at age 16, he's living with his mother in Liberty, Clay, MO. Apparently some money in family as mother shows $10,000, John and two sisters each have $4000. No father, perhaps dead.

In 1870, he and family are in Deer Lodge, Montana territory. He is a lawyer and a miner, $25,000 real estate, $8000 personal property. Shows he has four children already, oldest is five so he may have married in 1865. Wife was from MO as well.

If anyone is researching him, there is a lot of info on him at ancestry.com