What if the person who wrote in the margin didn't check the book out? Not all people are clever, but that would be the smartest thing to do if one simply had to write in the book.
Then the fishing expedition will catch no fish.
But just assuming that the person with the pen didn't check out the book, doesn't mean one shouldn't check it out to make sure.
There is no FBI list here. Only a library's list of people who checked out a particular book that happened to have something written in the margins. Something highly suspect of having been written by a terrorist. For all we know, it was someone who was writing a class assignment on OBL who jotted down the quote in the margins so it would be easy to reference.
So long as the FBI attempts to have probably cause for asking for privileged information I won't be worried. It is when they stop caring for such niceties that we should worry. So, I agree that the librarian had every right to challenge the request, but to deny it after being presented with what appears to me to be a reasonable example of probable cause, I think the librarian was just a foolish political hack.
However a thorough investigation (if such were warranted, which is unclear from the article) would require that likely leads be checked out. If the terrorists who rented the Ryder truck that blew up in the original WTC attack were stupid enough to return to the rental company to get their deposit back, then clearly it is plausible that the genius who wrote the "threat" into the book may have checked the book out using their real name and library card.