I am almost certain that the Joseph Pratte that was killed was the one for whom you gave the census information.
His father and other family members operated a river landing just south of St. Mary's Landing in Perry County among other businesses.
I could find no military service for him but he can be found in the Provost Marshal records in 1861, 1862, 1863, and 1864.
He apparently was arrested in October 1861 and some of the later records are requests to get his parole extended beyond Perry and Sainte Genevieve Counties to pursue his business.
His uncle Charles H. Pratte was killed by the Perry County Militia in June 1865 while he was being transported to Bollinger County. Charles had served under General Thompson and I do not think that there is a record of his surrender and parole. He may have deserted.
The Prattes were also cousins to Francois "Frank" Valle who was probably the most notorious of the Perry County Confederates. He was an officer in the Missouri State Guard and later in the Confederate army. He was captured at least three times and spent some time in the Alton prison.
I will check to see if there were any 2nd Missouri veterans living in Perry County at that time.
Thanks, Fred Eggers