Let me first clarify that Stella Polaris is an open source game distributed under the GNU GPL license (can be found on the website of the Free Software Foundation or FACF). This means the game will be freely available and distributable, as well as the source code. The user just has to accept the GNU GPL license in order to be allowed to play and utilise the source code. So this means StP isn't freeware, except that it will be available for download free of charge.
The reason why the name has been changed is that the name FreeAC was actually a temporary project name that was used longer than planned as there wasn't pretty much anything done for solving the name issue before I entered the team. The reason why the name was changed is that the name FreeAC refers to Alpha Centauri, but as this game isn't a SMAC/X clone, the name would only make it sound like a cheap SMAC copy as an open source game. Also FreeAC would have related us abit too much to FreeCiv as we're trying to keep a distance from being connected to other projects. And the name FreeAC could also be associated as a SMAC clone, as FreeCiv refers to the fact that FreeCiv is more or less a Civ clone with several modifications, while Stella Polaris is a game that will be developed starting from the basics and advancing to the most detailed issues, utilising ideas from many different games (the most recent trun model has even influences from RoN, but mostly ideas that have been found elsewhere are from SMAC/X, MOO, Civ II & III, Stars! and probably other games too). So the name FreeAC would also be misleading as it refers to a SMAC based game. Also a reason for the new name is that the name FreeAC do sound quite boring after all, as there's already so many games named "free", while the name Stella Polaris is more inspiring (okay, I admit, perhaps it has a certain influence that I was the one cracked the new name
) as it has a background too (read the part of the "FreeAC -> Stella Polaris" thread that talks about why this name was chosen).
The origins of the name FreeAC actually lie most likely in events that are unknown by me, but I guess Blake or Closey could enlighten more about the origins of the name "FreeAC."
I hope my answer was clear enough.
I will add parts of it to the FAQ as I get the first edition ready.