The thing with G. I. Joe, like a lot of other Sunbow-produced properties (Transformers, Jem, My Little Pony, Inhumanoids, etc.) is that the "moral messages" went above and beyond the two-minute snippet at the very end.
In many instances, the entire episodes of these shows - which were very often written at a higher intellectual level than what most shows of the time mustered up - had moral messages of some sort at their core.
For example, one of the most famous episodes of the 1980s G. I. Joe series is "Nightmare Assault." The plot is that the bad guys have developed a device that allows them to manipulate a person's dreams, resulting in nightmares so terrible that they're psychologically devastating. The resident sniper, however, has spent his life dealing with post-traumatic stress disorder owing to his verbally abusive father; nightmares are nothing to him, and in fact he's learned how to fight back. In the process of him facing down his own issues, he ultimately encourages the other heroes to willingly face their own nightmares. The heroes succeed, not only becoming much braver for having done so but also causing a backfeed that results in the mad scientist operating the machine choosing to destroy it.
The episode that aired afterwords - "Second-Hand Emotions" - had a similar plot: the bad guys developed a device that, when attached to a person's spine, caused their nervous system to misfire; this resulted in people panicking over the least little thing. The affected heroes literally had to stare down their worst fears in order to make it through. Interestingly enough, these episodes first aired on the 30th and 31st of October, 1986.
Joe Guide.com (formerly QK Theatre.com) This fan-produced site contains episode guides for the original 1980s G. I. Joe series, complete with detailed episode summaries. It takes a while to get used to the navigation method, however.
Transformers wiki A fan-produced Wiki site (which I myself did contribute a little to) that catalogs everything Transformers, from the original 1980s series through to today, even going so far as to record information about the toy industry itself. This includes episode guides for the original 1980s eps. Please bear in mind, however, that as this site was written for older (20+) fans, some of the humor is a bit on the mature side. Additionally, you do not want to read anything having to do with a Japanese-exclusive series known as "Kiss play" if you wish to retain your sanity (fans the world over hated it, and for good reason).