Perhaps something along the lines of a Surety bond could help? The couriers each put up an amount of money (BTC) as collateral for carried packages. This may also help with the repudation problem as it is easier to prove that money has been put in escrow than it is to check a person's honesty. Also should help with bootstrapping repudation. Not quite sure how it would work if a third-party grabs the package at a dead drop.
The risk of an unrelated third-party stealing the package should be small, and easier to deal with.
The main problem for which I haven't yet seen a good answer is infiltrated law enforcement, particular those wanting to build reputation before attacking. Suppose they don't care about giving some money to the system (escrow that would be taken from them). And suppose they are willing to deliver a few packages before attacking.
How do you protect your runners from them when they decide to drop traps?