This is really where politics and different types of bounties would be good. System wide, faction wide and galaxy wide bounties. For instance, if you have a bounty in an independent system, since it's independent, it will only be a bounty there. That system has no extradition treaty with any other system. If you have one in a system aligned to Ffederation, you should have that bounty in all systems aligned with the Federation. Create some political lines in the Bubble. Make a faction have some meaning.
As Stigbob said, as an Imperial, you could go into Fed space and tear up the place and retreat back to Imperial Space and be legally protected by the Imperials. As someone aligned to the Federation, you could go into Imperial Space and try to blow this CMDR out of space, and enjoy the exact same protection retreating to safe Federation Space. Ideally the Federation would award you for dealing with one of their enemies, while still getting a bounty in Imperial Systems.