The original names been Ishmael for Malta and Madrid for Crete, maybe that helps making a better distinction. There used to be infocards on Malta that referenced to a not small part of the people being catholic, but for some reason this infocard seems to've gone.
The Mediterranean Sea region of Earth is basically the origin of both Maltese and Cretans, so their planets and stations are christened with names from that whole region as the people on the Hispania been from all over that region.
The difference is that when the Hispania was sabotaged, some decided to stay with the wreck and the nearby planet, while others decided to move on. Those that stayed became the Maltese, those that moved on the Cretans.