This episode crashed and burned, and really ought to be retitled, "Black Mark--on an Otherwise Great Series". The military is requested to help remedy a situation with black marketeers. (We haven't really heard of this being a problem before, mind you.) Apollo investigates, some people die, the black marketeers are slapped on the wrist, and we are back where we started as if the episode never took place.
"Black Market" is a great example of a "filler episode". Problem, plot, and solution are all synthesized for one episode, and then never mentioned again. Another classic "filler episode" is this season's "Scar", which at least had some cool space combat action.
Just assume this episode never happened (and assume that the commander of the Pegasus was replaced by a new actor), and BSG will continue to be a gripping, groundbreaking series.