SeaGull,
First and foremost, congradulations are due to your son (and you!) for the committment to Scouting and a quality program. I've seen many teenagers who are treated unfairly, never look back (Youth groups, church, sports teams, Scouts, etc.).
Second, (this was a lot to try to digest in one sitting), there was a lot of good advice given (some better then others) as to the way your son (and you) should handle this, but, from what I could tell from your postings, he did what he was suppose to do.
The SM should not have been yelling at the scouts, it was not HIS training.