As to why the article does not use the word boy:
1. As I said, such terms are usually used as endearment, for the group you belong to. Phrases like "Us girls can program, too", or "Boys, let's go get this YC interview" are common and you cannot replace women and men in these contexts. I think the OP was using girl in this sense in her post.
2. The correct counterpart to the use of girl seems to be guy (although there are phrases like "old boy's network", etc.) mainly, I think, because of alliteration. Some opponents to sexist language are offended by guy, too.
To reiterate my point, as hackers let us think about and then act rather than regurgitate rules that may be dictated by others. Let us not do simple string matching for offensive words but set our regular expressions wide to check the context that words are being used.
P.S. An interesting parallel to this discussion would be the debate on the use of the N-word, which is considered taboo by many but used by others freely.