A joint enterprise - namely, Gibney's documentary 'We Steal Secrets: The Story of Wikileaks' - sounds like a natural-borne partnership, which started with Assange's cooperation and access. So why has Gibney soured so towards his subject? It started so well, too...
"This was a real-life spy thriller, with a hugely compelling character at the centre," remembers Gibney, talking in London. "This guy with a laptop in his backpack travelling the world, exposing abuses of power.
"I thought he was going to be mostly good. I've been around long enough to know that no one is all good, and if they are, they're not believable or interesting. So I didn't expect him to be all good, but I didn't expect aspects of the story to be what they were."
Although the earlier parts of Gibney's film shows him in apparent harmony with his subject, in reality, it was never easy...
"He agreed to an interview, but it was for about 10 minutes. I'm not interested in 10 minutes. I've got plenty of sound bites from all over the world. He didn't like my initial approach, which was that I was going to make this film whether he cooperated or not. I was hugely sympathetic, but I wasn't going to make a deal, and he didn't like that at all.
"You have to make a deal with him, because everybody at that time was going to him, trying to make a deal. And the deal was "swear you'll be loyal to me and my cause and I'll give you access, and then you can use that access to go raise money." Well, I had the money, I didn't need his approval, nor was I willing to give him control."
Two men with much in common, but cooperation between Assange and Gibney broke down
If Gibney had already realised that his film wasn't going to be the simple David and Goliath tale of Assange versus the US authorities, he had to ask even more questions once he began investigating the Swedish accusations against the charismatic Australian, and spoken to some of the women at the centre of the charges against him.
"Because the Swedish part of the story had already happened, I thought it's naughty, maybe, I actually thought that was some kind of conspiracy, the timing seemed too weird," was Gibney's original perception.
"But Julian Assange, instead of saying 'I take personal responsibility for this, and I'm willing to be held to account personally,' he says 'This is nothing to do with me personally, and is all an attack on Wikileaks.'
"At the end, it was about him personally, and he purposely conflated it with Wikileaks, and therefore draws in a whole group of supporters, who have to support a lie, in order to support his truth-telling. And that seemed to me fundamentally wrong.
"You don't get to say, 'Because I'm doing a good deed, I get to do bad deeds.' I'm familiar with that line of argument from the Catholic Church. Look at the work we do with the poor. Can't you accept a few priests who fuck young boys? No."
"Thus, Julian Assange begins to take on the colouration of his enemies, and he becomes more and more like a spy and less like a journalist, or transparency radical."
Does Gibney believe, then, as Dorothy Parker predicted gloomily, that everybody becomes the thing they most despise?
"It doesn't always happen, but it often happens if you're not careful," he ponders.
"Look at the pressure Julian was under. He achieved enormous fame, which would have thrown anyone off balance, and there was pure vitriol directed at him, by US politicians and pundits, and also the state, so there were powerful people after him. It would put anybody off balance.
"At the end of the day, I can understand why he might have done it, but it doesn't excuse him."
Gibney acknowledges that the shift in his attitude towards Assange made for both new challenges in his approach, and unexpected opportunities.
"I included a lot of (fellow filmmaker) Mark Davis's material, because I felt he got close to Julian in a way I was not able to, and showed a pretty positive side of the guy, and I thought that should be in the film. So, although people say I soured on Julian, I still put a lot of that stuff in there on purpose."
On the plus side for a wider story to be told, the limitations around Assange forced Gibney to dig into the labrynthine saga around US soldier Bradley Manning, whose voluminous disclosures to Wikileaks caused Guardian readers to sit up over their cornflakes two years ago, and who is now serving at the American Government's pleasure in high-security.
"I realised that Bradley Manning had been roundly ignored," says Gibney now. "Initially, he was going to be a small part of a Julian Assange story, he ended up looming much larger, and along the way, we got the benefit of Wired magazine publishing his online chats, and we found a very lonely, misunderstood young man.
"One challenge was, how do you present a character who can't talk to you? First we thought of using an actor, but then we realised the mechanism by which his feelings were communicated in this very human tale were between two people who never physically met each other, so we embraced that idea."
Viewers of the film learn about Manning through a series of emails he sent which appear on screen, his voice is never even heard, yet it is clear where Gibney's sympathy now lies.
"I hope this film will protect Bradley Manning. The US government t will do what it will to keep him behind bars for as long as possible, but in the court of public opinion, I can hope that people will see that this kid was not a spy, but a human being who thought he was doing good.
"I presented him in all his complexity, but I hope the film achieves that."
And while Julian Assange stews on this latest examination of his cause, and Bradley Manning sits it out somewhere in America, Gibney, with his interest in abuses of power, has already moved on. So what's next?
'We Steal Secrets: The Story Of Wikileaks' is in UK cinemas from today. Watch the trailer below...