Usually the military doesnt pursue charges when it has been this long. However, he chose to violate the law and IMHO should pay some sort of penalty for doing so.
I heard of a case where an American soldier stationed in South Korea defected to the North in 1964 (when he heard he was going to be sent to Vietnam). His wife, a Japanese woman who had been abducted by the North Koreans (he married her after defecting) was eventually allowed to return to Japan, but he was afraid of being shot for desertion. When he finally went to Japan and turned himself in, they busted him to private, gave him a dishonorable discharge, and perhaps a short stay in the brig—in other words, a slap on the wrist. But they may have thought spending 40+ years in North Korea was punishment enough.
I was a recruiter in 1988-1990, from what i gather from the little information given was that he joined under the delayed entry program or DEP. Under that program you are not officially in the service until the day you ship, so if he never went back to the military entrance processing (MEPS) for the second time he was really never in the service. I had an issue like this where I recruited a person into the army, and he joined for a job that required a background check, when the check came back before he shipped out it was found that he had a parent that was still a canadian citizen and couldnt go into the job he chose, he then had the choice of choosing a new job, or I would have taken him as a loss and had to make up that person. This person chose a different job and still shipped out.