Well, clearly Alex decided he wanted to rewrite the game to include multiplayer, but he had repeatedly stated that Starfarer would never have multiplayer. Obviously, he couldn't go back on his word, so he changed the name instead. Now he's able to stick to his word and he's free to implement multiplayer into Starsector! Hooray!
Clever man, that Alex.
EDIT: (For future reference, my explanation for the name change is a joke. I didn't realize this disclaimer was necessary. Thought it was readily apparent.)