Membership in the Sons of Confederate Veterans is open to all male descendants of any veteran who served honorably in the Confederate armed forces. Membership can be obtained through either lineal or collateral family lines and kinship to a veteran must be documented genealogically.
http://www.scv.org/about/join/eligibility.php

I do not know how the militia is classified.
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To my knowledge proof of not having deserted is not a requirement. Such knowledge would be difficult to show as much Confederate documentation late in the war did not survive.

For information, the United Daughters of the Confederacy (UDC) denies membership for ancestors subscribing to the Oath of Allegiance to the United States prior to Appomattox.

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Here’s more on young M. W. :

Middleton, Marion Wesley: Co G 62nd Ala. Inf. Enlisted Mobile 1865 served until paroled at close of war at Marion, Ala. 1921, RDF 1, Box 72, Garland, Ala. Born 1 Nov 1846, Simpinsville, Ala., Monroe Co. Pvt. Enlisted 1 Jan 1865 Mobile, Ala.

Ooops! Lost the source document, sorry