After finding about 180 clones of the article cited, I caught the drift at LIS: It's the anti-gay nature of some of the selections. That's where the "harassment based on sexual orientation" charge (not "sexual harassment", which is also a crime in many states) comes from.

But the suggestion that created the furor was another one: The Marketing of Evil: How Radicals, Elitists, and Pseudo-Experts Sell Us Corruption Disguised as Freedom, by David Kupelian.

While the book has many targets, gay people rank high as a source of problems, with frequent implications of a gay conspiracy hurting society. Publicity material for the book blasts the gay civil-rights movement for changing “America’s former view of homosexuals as self-destructive human beings into their current status as victims and cultural heroes” and says that this transformation campaign “faithfully followed an in-depth, phased plan laid out by professional Harvard-trained marketers.”

Almost immediately, fellow panel members (and soon others at the university) not only objected to the book (which never seems to have been in serious contention for freshmen to read), but to the idea that it would be offered for consideration. It was called “homophobic tripe” in one e-mail, and others noted the book’s lack of scholarly rigor, the statements in the book about gay people and others that have been widely debunked, the impact that reading such a book would have on gay people at the university, etc. As these e-mails escalated — with many of them circulating on the entire campus — the Faculty Senate considered filing formal charges of harassment against Savage. In the end, two faculty members charged him with harassment based on sexual orientation. The complaint said that gay faculty members were made to feel unsafe by Savage’s advocating the book as a reading assignment, and others questioned whether they would feel comfortable sending gay students to the library or encouraging any student to research gay-related topics, in light of Savage’s role there.[emphasis mine]

and

One professor who was willing to talk on the record was Christpher Phelps, an associate professor of history who has not played any role in the complaint.

He said of Savage’s nomination for the freshman book: “It was a ludicrous book to select and the idea that a chief reference librarian would be proposing a book full of homophobic nonsense was deeply disturbing to the faculty.” Phelps said it was important to remember that there are relatively few out gay faculty members at the university and that they face hostility in the region.

Both quotes from "Tolerance and a Reading Selection", from insidehighered.com, 14 April 2006.

So it also appears that the librarian's religion has nothing to do with it, but his professional judgment has been called into question. If a librarian is considered to be a threat to any class of clients, he or she is a liability to the organization that employs him or her because it's then impossible to do the job effectively.

Still wrong to file charges against him for stupidity, but not nearly what was portrayed in the Professors Hate Us right-wing blogs.