Well, yes - if an individual cashier calls them "girl" and "boy" toys, that's not necessarily the company's fault - it's more a symptom of a societal thing, and you're right, it's just a symptom. I don't see one woman's letter as a major thing in the grand scheme of things, but I do agree, the whole gender stereotyping toys thing is silly.
As a company, they may know that one kind of toy does indeed appeal to girls more and another to boys. Maybe that's because other people have given those kids those kinds of toys in the past, in which case it's society again, but still, from their point of view, that's the way it is so it's good business. If they stop calling them "girls" and "boys" toys, though, at least they aren't contributing to it (as much).