It's not really a hypocritical thing on FF.Net's side, but rather a lack of attention on the Moderators or Admin's part. Like i don't think it's just one or two guys going through the entire website looking for that sort of stuff. You're friend had the misfortune of just being the one that stuck out and a mod saw it. Again just because one mod enforced the rules of your friend doesn't actually mean that they go through the entire website just to find those kinds of fan works.
I'm sorry if i'm coming across douchey, but there are several things wrong with what your friend did. He/She wrote the fic despite a warning being given as you register and there are other sites where people can write fanfics about whatever. Archive of Our Own comes to mind. maybe there are sites specifically for that series' fanfics IDK. But yeah, is it unfair? yeah, but they aren't really hypocritical. at least i don't see it
There are a lot of problems on the site, inconsistent moderation is only one of them. I personally don't like how they outlaw certain styles. What they call "interactive entries" may be annoying, but they're still a form of creative writing (I even had to read a book series in college written as a chat script).
But I've never harmed an onion, so why do they make me cry?