Perhaps making a 'one-way' phase lane would solve the problem? Have the base attached to a planet and give that planet a super version of the phase jump inhibitor. Something like 10000%
I'm not sure what that would do to pirates returning from a raid, but they don't -have- to return, do they?
Also, keep whatever they are attached to out of the way from the rest of the map somehow, so it doesn't interfere with the gameplay too much.
Can you give space junk abilities? If so, make a custom space junk called Pirate Trap or something like that.