The NBA and the disgraced ref maintained that he bet on his own games, but did not fix outcomes.

The ESPN article argues otherwise through statistical analysis of foul calls as well as investigative reporting with the other gamblers and bookies in Donegha's circle of corruption. Based on their statements, it's rather conclusive that he skillfully manipulated games, although he couldn't control every outcome.

The article also highlights an unfortunate situation where Donaghy told the FBI about other crooked refs, but the FBI briefed NBA commissioner David Stern about their investigation early on, while it was still ongoing.

The investigation was then leaked to the press (strongly implying Stern did it). This made it impossible for Donaghy to wear a wire since he was now disgraced and fired from his job, and the NBA maintained that Donaghy's was an isolated incident of one rogue ref placing bets but not affecting games.

That's my summary of their reporting anyway. I found it persuasive.

I think the article makes a pretty persuasive argument for the relevance:

"It matters all the more now. On May 14 of last year, the U.S. Supreme Court struck down a 1992 federal law that had forbidden states from legalizing sports gambling within their own borders. It's widely believed that the ruling will lead to a lifting of the interstate prohibition on sports betting, which, in turn, would give rise to a massive increase in the money wagered on American sports. At the same time, the NBA -- which once balked at gambling -- has now openly embraced legalized sports betting more than any other U.S. pro sports league. In 2014, commissioner Adam Silver penned an op-ed in The New York Times advocating for legalization. In July of 2018, he announced a multiyear deal for MGM Resorts to be the 'official gaming partner of the NBA.'"

The author put two years of work into reporting it. A lot more detail and strong evidence that contrary to what was claimed 12 years ago, Tim Donaghy was throwing games.