The article gives rather short shrift at the end to what seems like a pretty strong argument against this theory, which is that it isn't clear what it would get the FBI. Is there any info they can get from running the site that they can't from just logging torrent traffic?

Plus, while the FBI is allowed to facilitate minor illegal actions during under-cover operations (like having one of their agents work as a mod at Silk Road), this would involve them essentially paying for and running the infrastructure for hundreds of thousands of acts of piracy. I'm pretty sceptical the people in charge would sign off on that, especially if most of the information could be gathered using other methods.