I say take back the names
Make changes if needed and put in better checks to insure it doesn't happen again.
Many players jumped in and created guilds using the names, knowing full well that the original intent was to allow players to either join a guild or join an organization within the story line. They did this knowing that they could be forced to change it later, or perhaps wanting the confrontation between the "evil" Funcom and their "good" guild. What motivates some players to deliberately choose one of these org's names could be anything from adoration, intrigue, to flat out brashness or contempt. No matter what the motivation or intent - it's time to set things right. Many players would like to be in Omni-Pol, or Omni-Med, or The Sentinels, but want to be a part of the GAME's org, not another player's org. Fix it now and let's move on to the next issue...
GM-run story clans are the way to go
When the game first launched a large group of us wanted to join the Knights, based on the description given in the game manual. When it was obvious that wasn't possible, we decided to form a clan to get organized for the time (we thought it would be September of last year, oh well) when the NPC clans would be opened. We did this because we did not want to fall behind the "established" player clans when teh NPC clans finally opened up. From a role-playing standpoint I served as Lord Galahad's "steward", handling the day-to-day operation of the clan until his return from planning sessions with the Council of Truth.
As the leader of that clan, I can say emphatically that I strongly support Funcom taking back the names and creating GM-run story organizations. It has been in our charter from the beginning that we would play as the Knights, and would disband and join the "real" Knights when that option became available.
I'm glad to see the majority of people on this board agree with that! Please, Funcom, make it so!
Kat