I think that's part of 'adventure'. Rule number 1 of the scoundrel, Be Sneaky. Rule number 2, Don't Get Caught. Rule number 3, RUN.
As much as there's an Imperial border nearby, and in many campaigns you are well within Imperial borders, not every encounter involves Imperial fleets or squadrons or... any Imperial vessels. Refs bring out imperial assets when the plot needs it, usually when you are trying to drive home the point to players "NO mean no!". You don't overwhelm players in encounters you supply a reasonable or slightly unreasonable opponent. That will mean the vast majority of the time even pirates will face planetary navies and security forces with the occasional subsector unit for something more determined but not for a slaughter any more than any other campaign type. A subsector frigate should mean the players have been getting unreasonably.... bold in their actions.
