I believe it costs merits, not EC to change a ship name. Simply lower the merit costs of changing a ship's name; either across the board or by tier. Merits are dear to a low level character and he probably can't afford to rename each ship as he ranks up but merits become trivial at the top rank. For now, making it easier for lower level characters to rename their old ships lets them keep them and still keep their favorite name for their new ship. The "real" ship name should be your top level one because that's the one you don't grow out of like the lower tier ships. I quit using my favorite names on my Miranda because I couldn't afford the merits to rename them 20 hours of gameplay later when I got my tier 2 ship. Making it much easier to rename the lower level ships would be an easy fix for the problem, at least until they decide to add the registry to the ship's name for game purposes.
You're right.. it is Merits, I think if it was EC it might be easier to deal with.. but you're right, merits are too had to come by at the lower tiers.