Well, I think staying because she's there is as solid a reason as any.
If that Vanilla tag wasn't there, I might have suspected that maybe part of her work is to make sure (male?) employees don't get so frustrated that they leave their job, but I'm glad that doesn't seem to be the case.
What especially throws me off here is the implication that he goes from a crowded room where he was chewed out in front of a handful of other employees immediately to a break room where he whines and the heroine comes and starts sucking him off right away. Like, I know there's only 16 pages, but damn! Aren't they still at work? Isn't everyone else just one room over maybe still milling around after the public haranguing? You expect me to believe the two of them start boning down right in the middle of the break room where literally anyone one room away could hear/smell/walk right in on them for no more compelling reason than the break room is a completely normal place to hang out for a few minutes on the job?! She even tells him to shush on page 3 and by page 8 they're making all the usual noisy hentai sex sounds.
Part of me says: "Smells Like A Trap!", i.e., to put it simply, Fujiyama-san seemed to use "me so horny seeing you work long and hard, etc" to (cough-cough) convince Naoe-kun to stay there, even if he has to put up with abuse from tyrannical boss (boss's behavior may or may not be justified, since story doesn't go too far in that regard).
It may be Super-Effective, but honestly ... Not Sure I Add To Favorites.
If that Vanilla tag wasn't there, I might have suspected that maybe part of her work is to make sure (male?) employees don't get so frustrated that they leave their job, but I'm glad that doesn't seem to be the case.