Anime / Manga - Sad Office Lady with a Hay Fever.

Okay, at this point it really does seem to be a Japanese sub-genre of kafka comedy where specifically a cute and nice girl is tormented.

That's just normal kafka comedy. Japan apparently decided they needed a genre which applies that to cute and innocent girls who never do anything to deserve it, taking moe to the extreme by making them so sympathetic and huggable that you want to strangle the author just to make the emotional torture stop.