Excellent points. you had some great NCOs, that is for sure. As we say in the Army: NCOs are the backbone.
You are right about running everything up to the Commander being a waste of time and resources. I believe good leaders can accomplish these things on their own, but there are the occasional problem children that aren't worth the effort or haven't learned after some wall-to-wall counseling. For them a quick Summary Article 15 may do the trick or even Company Grade Art. 15. After that, chapter the guy out for the good of the unit/service.
I hope the Marine you wrote about turned his life around for the sake of his family and the unit.
Behind the motor pool is always a good counseling area. Lots of privacy to get the point across.
A related kind of funny story. I had one newly promoted goofy corporal. Cpl. Holloway. Apparently -- I only heard about this after the fact -- he was giving some PFC crap and ended up saying "lets step out back and settle this". The PFC was about 6'3 200, and I swear the corporal wasn't a shade over 5'8", maybe 155. And the PFC promptly whipped the crud out of the Cpl. The senior SNCO's basically said the Cpl. deserved it, so I let it go. But talk about ruining your credibility....