There are depots outside bases like Barrier Gate, Heisenberg and Newport that you can shoot to lose rep with the Freelancer faction. Just be careful not to go red or undockable in the repsheet.
Make sure you will respawn on the FL base so when you come back just hit the bar and look for FL bribes. 3 big ones are what you want to see, tht should give you full FL rep again. Odds are for it to work best you will have to go to total neutral but not lower. The base will shoot you of course but after you get the fix its back to normal.