Let's clarify: are we talking about renaming star systems, or renaming individual planets within the star systems? My own practice has always been to rename each star system according to various schemes (I have several, depending on what I feel like using at the time, and which I may discuss in another thread); I think that you can only rename a star at the time you colonize it when the popup appears saying you've discovered a new solar system.
As to individual planets, I remember that this could be done in the OS/2 version. It's been several years since I've played that version, so I don't remember exactly how it was done, and I haven't tried my first game of version 1.01 with Bonus Pack added yet (Real Life calls, don't y'know) but will do so this weekend.
-Joe-