There is a difference between individuals and names of states, cities etc. Individual persons are responsible for certain actions. To name a ship after them, honours them. The same is true, if ships is named after battles or political symbols. To use such a name, is a political symbol and always was a political symbol. It was never neutral. Those, who had chosen names associated with the Confederacy, did that, because they wanted this association - or at least, they had decided to ignore parts of the biography of certain persons (e.g. Maury). The use of names associated with the Confederacy was symbolic, probably to appease far-right wingers in the South.

In contrast, the name of states or cities is usually not a political symbol (there are exceptions). The name is politically neutral.

The exception would be e.g. a name of a city, which today is in a different country. That would be a highly political symbol, e.g. if today the Royal Navy would use names of Indian cities or the German navy would use names of cities today in France or Poland.