He didn't lose the kid.
I don't have time to read all the answers, so apologies if this was told to you, but Michael left the camp during a time when every camper and staffer had just finished eating lunch together. Those that went on the hike, in other words, RETURNED, then they all sat down together for a meal. It was at the end of it that Michael got away from the group without being noticed by the others. By the time it was known, they weren't able to find him nearby and a big search was called for.
His father says Michael told his family afterwards that he was upset that his close buddies in scouts didn't go on the campout and he felt homesick. He was determined to leave and find his way to the nearest highway to flag down (hitchhike) a ride back to his home. Father said he would have a series of long talks with Michael about NOT hitchhiking (as he said he already had done but will repeat and repeat).
Others in charge at the camp said Michael did not want to go on the hike and pled exhaustion and the need to sleep in. Now I say, if he was bummed because none of his friends were there, it makes sense he wouldn't want to go on a demanding hiking trip with what he saw as a bunch of strangers.
You are correct that rules prohibit a single scout and a scout leader from spending time alone. There was a BIG problem, though, because Michael's intransigence about not going with the others put them in a terrible bind. Were they to cancel the hike for EVERYONE?? Yes, that has to be addressed, but not because the scout leader should be under suspicion for doing something to the boy. Not from what is known so far.
Ah, that's right, he didn't leave until after the group had returned. Though he still had quite a lot of time alone with this adult. Odd that he waited for the group to return, if he'd decided to take off. Maybe the adult WAS keeping a very close eye on him, and then once everyone was back it didn't seem so likely that he'd leave, so he was no longer being watched so closely and grabbed the opportunity to make his run.
I get the part about breaking the "never alone with a kid" rule out of practicality -- I'm not sure how many other adults were on the trip, but perhaps not enough that leaving two behind with this kid would enable sufficient supervision of the hikers. BUT if the situation with the kid was so bad that they felt they had to break that rule, they definitely should have called the kids parents to alert them to what was going on, and try to arrange to have them come pick him up nearby. There's no indication that that happened. When it's no longer possible to supervise a kid within the rules, the very least that needs to be done is to notify the parents, and in the age of ubiquitous cell phones there's no obstacle to doing that while on a camping trip.
It does sound like this kid isn't quite all there, and that the parents and scout leaders may not have been facing up to the degree of that problem -- you just can't make things okay with a mentally disabled kid by pretending he's normal and having him participate in everything the other kids do as if he was normal. Twelve is awfully old to pull a stunt like this without some major extenuating circumstance like being molested. My gut feeling is that this kid is seriously troubled for some unknown reason, in addition to not being of quite normal intelligence.