I dunno, the legalities of it are quite a grey area. They may be reluctant about the whole thing as it may drawn unwanted attention from copyright holders. Authors and archives of fanfiction and transformative works live in constant fear that they're going to be the target of a lawsuit from the owner of whatever fandom they're working in. While all your script is doing is presenting the same information in a different form it's still the kind of stupid distinction that can lead to trouble. The argument the copyright holder might put is that this is more like a book, while the HTML on the website is more like a forum post, or some other such nonsense argument. It doesn't really have to make sense, it only has to result in a legal threat for it to be a major problem. Fanfic sites tend to jumpy about this sort of thing because they're in no position to put up a fight, so they'd rather not tempt fate, no matter how entrenched the concept of fanfic may have become. Having said that, they may not be bothered about it at all, so I think you should ask them and see what they have to say.
The major technical issue I can see them having is the potential for thousands of users to bombard your site to get eBooks and your grabber then making thousands of requests to their server to retrieve the text for them. They'd be worried about getting flooded.
I'm pretty positive about this project in general though, I think this is a great idea. Even though I don't use Fanfiction.net much myself, I do love fanfic (no matter how much rough I have to wade through to get to the diamond). I actually had the thought the other day that it would be great if FeedBooks made their engine code available so that fanfic archive software like eFiction could incorporate it and provide users with a variety of eBook options to download their fic in. But if we can't have that, then grabbers are the next best thing.
