The order to disband the 5th MSM Cavalry (Old) on Feb. 4, 1863, was not specific to that regiment. The entire Missouri State Militia organization was being overhauled from top to bottom. For more on this, see http://civilwarstlouis.com/militia/federalmilitia.htm
As of Feb. 4, 1863, Companies A, B, C, D, E of 5MSM(Old) were to be integrated into the 1st MSM Cavalry, while Companies F, G, H, I, K were to be integrated into the 9th MSM Cavalry. That all changed as of March 13, 1863, when the Union command basically said forget about that--send them home instead.
"Twentieth Century History of Carroll County, Missouri," Volume 1, published in 1911 and written by S.K. Turner, at page 266, sheds light as to why the Union command changed its mind--"...The regiment gained for itself much unfavorable notoriety. It was known and is still spoken of as 'Penick's thieves.' After being in service about one year, it was mustered out at St. Joseph, 'in view of the interest of the public service,' as the order of the commander-in-chief stated, and it is stated that this was because of the reputation of the command for lawless insubordination and conduct unworthy of soldiers generally...."
Once the troops were mustered out of the MSM, as able-bodied loyal men, they would have been required to enroll in the EMM (again, see http://civilwarstlouis.com/militia/federalmilitia.htm).
If you have not already done so, you might contact the National Archives and obtain a copy of Henry and A.J.'s military files. That might shed some light on what was going on with them. Also, check to see if there are pension files for them--those would contain affidavits and if the issue of the desertions was still unresolved at the time the men applied for them, there would probably be a considerable amount of detail regarding what had transpired.
I would say your analysis regarding the mindset of the men who joined the MSM is pretty much close to the mark.