Fort Worden is apparently the only US Army base to ever be named after a Navy officer, one John Lorimer Worden, commander of the Monitor in the US Civil War. The reasons why are possibly lost to history. Any military history buffs out there who might possibly know why?
One supposedly plausible answer is that a president of the day belonged to a secret society (presumably in Washington DC) where they were having a meeting or panel and Worden's name was tossed into the hat as they were discussing historically relevant names to use in naming things. I'm not sure of the name of this society, but the time frame would have been late 1800s, pre-dating Fort Worden itself by an appropriate amount of time.
Warning: This question may actually be unanswerable. It has puzzled professional historians.
You are probably on the right path with the secret society idea though the society I suggest wasn't exactly secret. John Lorimar Worden, Thomas Lincoln Casey, and Daniel Webster Flagler The three individuals with forts named after them in the "triangle of fire" were all members of the Military Order of the Loyal Legion of the United States. Though practically every Union war hero also was as were several presidents. In 1893 The Quartermaster General Richard Napoleon Batchelder suggested that all forts be named after war heroes. It's possible that the suggestion made it's way into a list for use by the Secretary of War. It's also possible that the list was composed by the Military Order of the Loyal Legion of the United States.