Alright, you did have some very valid points in your text about having a right to feel/be a part of the situation rather than just a target dummy. I just want to clarify that I have my opinion, but that I am open to it being flawed.
Once this trial has sort of settled in, and all different strategies have definitively been proven fruitless (also advanced escorts and whatnot), perhaps the introduction of a new ship class with a price tag like the barge (so only few people opt to pilot it) that handles like a true battletransport (very heavy armor or perhaps a BS shield, more guns) for high-risk trade missions would do it? Make it so big that it is vulnerable to novas to retain some balance, but make it a beast of a transport able to stand a chance at running vs a cruiser? Problem is that everyone would probably get one, further escalating the application of force used in piracy.
I mean I would really like to see a game balanced so that different ships would be optimal for different routes and commodities, rather than "one size fits all" (5K). It would breathe some life into die-hard trading factions, and I know some (like the Bowex Clydesdales) do it for RP but it would be nice if there were more practical reason to not always use the 5K'er.
EDIT: I know you know your stuff at |IMG, but have you tried using cloaks on scout ships? Your transports in the convoy could carry a portion of fuel and supply scouts with it, so they would have a large operational range. Your scouts would effectively get a "get away free card" vs. any nasty surprises that might show on the other side of the jumphole.