Mooster, I tend to build 4 Starbases in the Sun gravity well of each star system I inhabit... this also helps slow down the enemy or pirates while I decide to reinforce that area with a fleet or let my planetary defenses do their work alone...
But if the Trade/Refinery ships had a laser a hair weaker than the Colony Frigate, or even just a single flak cannon could ensure some survivability out of those civilian ships... But if you are using the Distant Stars mod... they have more armor than pirates do so I guess in the end it comes down to the research balancing.