I think we're over complicating things. 
The basic issue is "Player infrastructure needs to be vulnerable". This is to allow for monsters to do more than simply attack units but actually have a significant effect on the short-term game as well as to allow for factions to hurt a superior foe without necessarily engaging in combat.
Rather than attempting to add micromanaging on to the caravan system (and really, it is because are you ever -not- going to protect your caravan?), we should address the issue and see if the system itself isn't a problem.
What if instead of routes/caravans being distinct units after a trade route is established, the route is automated. Bonuses happen as they do now, but instead of a caravan traveling, the route upgrades overtime. No units running around. However, now, monsters can 'attack' routes themselves. Monsters within a certain radius of a route as well as monsters 'guarding' or pillaging a route apply a cumulative penalty to the bonuses of that route as well as the upgrade time. After a few turns, the penalties offset the bonuses. Factions and monsters can also outright destroy a section of road to force re-building. New technologies could add effects to caravan to counter-act monsters in the late game (Armed Trade Routes: Monsters take damage over time within a certain radius, etc).
Same overall effect as monsters attacking caravans and having to defend them (you still have to go out and clear out monsters) but you don't have to keep track of producing 12 units for every route, making sure they're all up to date in tech and unit number, etc etc etc.