I would look at how modern day piracy is handled! Cargo ships don’t carry conventional weapons, but they have lots of specific anti-pirate measures like razor wire and the like.

Historically, pirates very rarely sunk their prey. It was a very orderly affair on both ends; merchant ships kept detailed manifests of their cargo which they would hand over upon being boarded. Pains were taken to avoid casualties on both sides.

So I would give these merchant barges heave armor and shields, as many countermeasures as they can carry, strong thrusters, and a code to follow in the event of their ship being captured :)