Just don't play with them.
Which now sorta stinks because you can't play random. I *wish* IC would simply change the modifier to StarBasesCanHyperspaceWithPhaseNode or StarBasesCanHyperspaceFriendlyOrNeutralSystems. I favor StarBasesCanHyperspaceWithPhaseNode because it requires additional setup by the Vasari player to pull off and is still extremely powerful once it's acquired.
Essentially the phase node approach would still allow you to attack with starbases, but would require kosturas or a level 6 Antarak or phase gate to perform the jump. The main gameplay mechanic here is a retreating fleet doesn't have to worry about be destabilization and being attacked by the same starbase as it jumps to your world.
Now you may argue this doesn't make any sense, why can it only phase jump to certain systems? Well, it's called balancing and there are lots of other things in the game that fall in that category. You can't phase jump across stars with phase gates or phase nodes from kosturas for example. You can only build one starbase in a gravity well, though you can have up to ten or more now if every faction built one on a planet.
The key to me is a fleet should be able to flee from the starbase without immediate fear that it will not only destabilize it's hull and am but will also immediately jump in after and finish the job.