Maybe make this another choosable option on startup? The longest thing to implement/do would seem entering whole bunch of names that the game would have as a Serious/Realistic Star Name Database that it would use if the Players chooses. This would maybe end up as various combinations of Letters and Numbers (welcome to XLFVPT Star 42 , sorry XLFVP..S Star 41? Um, 400,000,000 miles over dere, go thata-way 100,000,000 miles, turn left at the black hole, run like hell past the Drengin home system...Good luck, my good man!
I don't know about it breaking immersion (immersion breakers I love: the humourous/quirky tech quotes, the "pop-up" robot, the funny dialogue from other races ("I was just reading Toture Monthly'" from Kona...)), but if it's not too difficult to implement (doesn't sound it), why not make GalCiv3 as customizable from the Start Screen as possible (ie from "Funny As Hell" to "Gravedigger Serious" immersion sliders, etc)?
That said, I'm mortally offended that you would turn your nose up at the thought of colonizing my Homeworld Wishupona....