C. A.,
To find the outcomes of James Smith Garrison's courts martials, I recommend you try the National Archive and Records Administration files, probably under his name in files that pertain to only one person. Below is some detail about Garrison that may assist you to know when you have the correct file or not.
The 1860 census of Fishing River Township of southeast Clay County lists the very large W. Garrison family all born in Missouri except Smith's parents. William Harrison, 46 in 1860, a farmer with estimated $1,000 value in real property and $500 value in personal property was listed as being born in North Carolina, and Mary Garrison, age 42 in 1860, was born in Kentucky. The children are Wesley at age 21, Smith at age 18, R. (a boy) at age 16, Hannah at age 14, "G," I think (a boy) at age 11, George at age 9, Mary at age 8, Alice at age 6, Margaret at age 4, and I cannot read the name of a girl age 2. The way the census-taker scribbled down the Garrison children's names, often with only the first letter, I get the impression that he or she was in a hurry to get away from the Garrisons, but that is only my conjecture. I did not take time to notice, but maybe the c-t did that all the time.

Also in Fishing River Twp. I find Anna Roberts, age 18, born MO, as a servant in the Robert Moon household. I would guess this is the soon-to-be-wife of Smith Garrison.

I was able to find clues to Smith's military career in the online files of the MO Sec'y of State's office website:

His card in Company G, 2nd Missouri Cavalray Regiment (Merrill's Horse) had Smith Garrison enlisting 22 October 1861 at Chillicothe, Livingston County, and mustering in 31 October 1861 in St. Louis. I would guess that the regimental cadre took the Company G recruits by train to St. Louis for physicals, etc. before mustering in the men (who passed the physical, etc.), and that the regiment was equipped at Benton Barracks or someplace else in St. Louis before taking to the field. The only other notation of his card is that Private Smith Garrison deserted his unit 8 February 1862 at Columbia, Boone County.

Since Ray and Clay Counties were strongly southern in sympathy, I didn't have to look too far to find the correct Union "state militia unit" you mentioned. Private James S. Garrison enrolled in Captain Hawkins' Company D, 51st Enrolled Missouri Militia (EMM), at Richmond, county seat of Ray County, on 29 July 1862, which is about the start of the manditory enrollment begun across the state for the scores of EMM units in late July and August 1862. Some clerk struck out the "July" month on Private Garrison's record and it appears wrote in instead "Aug" for August 29 1862 for his enrollment and November 29, 1862 for Garrison's being ordered into active duty in this unit in Ray County, probably at Richmond, rather than the 29 July 1862 date for his start of active duty that was first typed on the card. I can go along with Garrison's being enrolled on August 29, but I cannot accept that he began active service in November 1862, since his data card also states in remarks that James S. Garrison deserted from Company D, 51st EMM on 11 September 1862.

I would think that the two desertions would bring a prison sentence, but if Garrison was convicted of being a bushwhacker in the 28 June 1864 Kansas City tribunal, he could have been executed. You may wish to look also at the "Daily Kansas City Journal of Commerce" in late June and very early July 1864 for some coverage of Garrison's military trial results.

I looked in vain in the online State of MO, Sec'y of State's Office website for Union Army Provost Marshal Records of Missouri for anything about a Garrison that corresponded to this man's name.

This is a challenging case, and I wish I could have found more information to help you.
Bruce Nichols