Now she remind me of a certain imouto in a similar hairstyle... Kyonko?
Kyonko got tired of Haruhi's shits so she became a shipgirl instead. Or Haruhi imagined the world being taken over by a mysterious enemy and now the Organization are running the whole Navy, having Kyonko being one of the shipgirls to fight them.
Whichever it is, it still makes a good crossover doujin. I think.