You should be able to give your ships an order to refuel from the civilian harvesters just as you would give them an order to refuel from your own tankers. Go to the Task Group (F12) window and make sure the Task Groups box is checked. The harvesters will show up as locations on the lefthand list, below the planets. When they refuel from the harvester the civilians will bill you. As far as I know there is no way to automate the fuel purchase other than having one of your ships cycling its moves between refueling at the harvester and dumping the fuel at a colony.
EDIT: spelling