In the interest of fair play, and to minimize angst, DDO/Turbine need to rename the servers when they are merged.
The main problem is that the "parents" can squat on guild names, it doesn't appear to take activity or legacy into the merge.
Some guilds do span several servers so they have protected themselves. Others don't or couldn't because somebody else has the same name. In some cases posted, the rival is totally inactive and is just depriving an active guild from its use.
Some guilds span games and their name also lets others who know them, meet back up, upon entering a new MMORPG, many have also extra resources into creating an online presence such as a web site.
The fairest way to handle this, would be similar to character name, where age (seniority), and player activity determine who gets the name.
As DDO may not have all that data, it may be harder to determine, but they do know who the founding guilds are and thats a start.
By prescreening the servers prior to merge they could identify guilds in conflict, and have an in game mailing alert them. The mechanism is there and used for updates already.
If there wasn't 2 or more responses or claims made in a reasonable time, the name would belong to the first claimant.
If there remains a dispute then they could use member activity (frequency of play), and the possible presence of guild/society websites, to resolve the dispute.
It is possible that the guild masters could be asked to try and reach an accommodation, but I think that would lead to goldfarmer like selling.
I realize this post should probably be in the merger forum, but there are already many like it there and Turbine has chosen to ignore them. Instead of having the decency to give a response.