What I often find myself doing is putting a few engines on my harvesters, giving them a top speed of maybe 500km/s, and have them dump their fuel at a moon of the gas giant, so they'll be away from work for no more than a few minutes, and I don't have to deal with tugs to put them into place initially.
Hrm. I've never done that with a moon before. It still means I have to take the time to go get the fuel from the moon, but it does have a good feel to it.
As for me, I usually make a fleet of huge harvesters and huger tanks with just one engine each (to be able to move just in case).
Once every 6 months or so, I have my main battle fleet (including tankers) dump 90% of fuel on Earth, refuel at the harvesters, then come back home.
As for civilian controlled fuel harvesters, I honestly didn't know that happened. Interesting.