C.E. Evans wrote:
There could always be a "Firefly-type" series that focuses on a civilian freighter that sometimes takes on jobs that aren't always on the up-and-up and may require them to fight their way out of situations that occasionally turn south on them. In that sense, Starfleet could be depicted as not the enemy, per se, but something the crew would like to avoid dealing with whenever possible.
At that point, using a civilian PMC or civilian equivalent of Starfleet would be preferable.
Running a freightor without weapons or very limited weapons wouldn't make as good of a base setup. Firefly worked well in that their usual solution was to run, hide, or evade attacks while airborne. While that is all well and good, if they were a PMC group with enough firepower, they could have interesting space battles.
Who said that all civilian freighters are unarmed? If they sometimes dealt with the black market, their ship could be equipped with disruptors, photon torpedoes, and even some stuff they'd don't want Starfleet to look too closely at. But even without a black market, it's also possible that civilian ships have to be licensed to carry armaments too, especially if they operate in regions far from the protection of Starfleet. In such a case, they'd probably just be equipped with standard phasers (in ENT, the civilian freighter Horizon
was armed with plasma cannons).