@FLEA
So I'll lead with this: I agree with you on the problem. ANY hierarchy structure that allows older/stronger to prey on younger/weaker is not a responsible structure. An argument could be made that in these JROTC units, even without rank structure...there'd still be rank structure in the form of 8th grade vs 9th vs 12th grade...etc. That's not going away. I'm betting JROTC definitely exaggerated the problem by providing a backed-up rank structure to work within. Yup. That's a problem. It's also been a problem in the active duty.
Your experience as an aircrew member is BY FAR not the norm in historical standards. Having a Col as a Nav who has to listen to you as an aircraft commander is overwhelmingly weird in the history of ranks structure, even in modern militaries. Because we're technicians who are also officers, things get sideways real quick, thereby making our experiences a poor example. 10 minutes of observing US Army up close will show that. Read your Robert Heinlein for excellent clarification about the heart of officership.
My real argument here is not the problem that you've admired and spelled out so well. My issue is with your solution. You point out a correlation (rank structure and abuse) that may, or may not, be causal. Contributing? Definitely. But there is so much cultural specific influence going on here that it's very difficult to breakout the root cause. The solution is very simply though.
Why, for the love of pete, do you come out with the solution of "ban all ranks in all JROTC"? Aside from the obvious fact that you don't like them because...well you obviously don't seem to understand them at a macro level (which is fine).
The obvious answer is shut those units down. Permanently. If they are a detriment, get rid of them. It's a localized problem that requires a localized solution. You don't kill a man for a broken leg. You deal with the leg. Your supported answer is akin to saying "don't ever let this man outside again". It's foolish and mis-aimed. There are plenty of JROTC units with NONE of these problems. You quoted 50% OF INNER CITY UNITS. That's a localized problem. What's the number come to if including all units nation-wide...which is where you would apply your answer? You are calling something systemic that is, in fact, due to a local unit culture problem.
Put in other terms, if 50% of T-6's go landing gear up, should we change to T.O. for every single airplane in the air force, regardless of their gear-up landing numbers? Or perhaps make everyone fly around with their gear down because retractable gear are stupid and I don't understand why we need them! The analogy breaks down, but hopefully you see the point.
The obvious answer is if the units are a detriment, shut the units down. The end. Instead you choose a solution that should be implemented country wide without any thought to 2nd or 3rd order effects.