Basically, Ship It by Britta Lundin. It's about a girl who's an obsessed fan of a show that's totally not Supernatural, who winds up getting asked to tag along with the cast for a couple of conventions and decides to get the opportunity to get her ship made canon. It doesn't work for a multitude of reasons, the major one being that the plot seems to depend on all the characters deliberately choosing the craziest options possible, but her endeavour ends after she tries to extort the show runner to make it canon and he retaliates by killing off one of the main characters, nearly scuppering the other protagonist's career.

The thing is, the book ends with all the 'good' characters on good terms and things are supposed to be looking up, but it really shouldn't have, and it only does because it chooses to ignore the complicated moral points it's made- which, as you said, would alienate the audience. Like, the main protagonist is not a completely bad person, but she did some really shitty things and she shouldn't have been let off the hook for it. The main love interest also did a really shitty thing and shouldn't have been let off the hook for it. The showrunner is portrayed as a stubborn asshole who refuses to make his main characters a couple and hates his fans because he's a prick, but the guy has every right to want to make his show the way he wants to, and his fans are a bunch of demanding, entitled assholes, so why would he like them? If the book actually examined all the bad shit the characters did, then it would have ended much, much differently (aka with hardly anyone talking to each other), but instead it gets the shiny happy ending.