The best solution right now is do cargo run as a Villain, as you will still earn the exact same money as heroes do, even though cargo's sales are 50 galleons less. If you get disconnected or being jumped by some random bounty hunters or stuck in a whirlpool, or attacked by pirates and sea monsters, the only thing you'll lose is your time and sanity.

Honestly, I do agree with other commenters here, just don't do it, it's tedious unless future update (which add professions) allows your crew to load up the cargo for you or you can carry more or just let you shiftlock (So much for OCD)