The TV Academy gave a show of support to HBO’s controversial Going Clear: Scientology And The Prison Of Belief, naming it best documentary or nonfiction special.

“This is a great honor,” said director Alex Gibney in picking up the statuette, adding the project would not have been possible without the “courageous support” of HBO execs. He also paid tribute to the “courage of witnesses who stood up against… the human rights abuses.”

Gibney’s film, based on Pulitzer Prize winner Lawrence Wright’s book of the same name, looks at the inner workings of the multi-billion dollar organization, using archival footage and interviews with former members. Ahead of the HBO debut, Scientology launched an all-out attack on the project, which details the origins of Scientology and its founder, science-fiction writer L. Ron Hubbard. This included challenging the reliability of former members who’d been interviewed by Gibney, including writer-director Paul Haggis, a prominent Scientologist for more than three decades before he exited the church in 2009. Scientology’s strong ties to the Hollywood community had been expected by some to work against the project at Emmy time.

“When I read Lawrence Wright’s book, it was very powerful both because it took on the human rights abuses of the church,” Gibney, who also won for writing and directing Going Cleary, said backstage, “but also the idea that very smart, very capable people can fall into this belief.”

As to whether he was harassed by the church, Gibney said, “Most of what I received were attempts to get into my head, myriad legal threats, none of which were made real … It wasn’t as bad for me as it was for some of the people who appeared in the film, who were subjected to harassment by private detectives, physical threats.”

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On the suggestion that Tom Cruise is largely being left alone by the media, he said, “I’m fairly confident that many programs who wanted to have Tom Cruise on their shows were told you can have him on one condition: that you not ask him any questions about the Church of Scientology. But what’s up with Tom Cruise, why won’t he address these things? … he received documented proof of these abuses.”

When asked whether the project had changed him, Gibney said, “What changed me was something odd … I understood better how it is possible to fall into a kind of belief system and end up doing things that are irrational because that belief system becomes part of your identity. I had to look at things I do in my own life as a result.”

Regarding a possible followup, Gibney noted, “There’s a lot more material already that I’ve received, more to come out — and so far the IRS has not revoked its [tax-exemption] protection so there’s a lot more to be done.”