After the storm erupted, the ABC's director of television, Richard Finlayson, issued a mea culpa for having Mallah in the studio audience rather than pre-recording his question about the citizenship changes.
Since then, though, it has emerged that the 30-year-old has made two previous appearances in the Q&A audience and has tried to submit questions on four previous occasions.
Abbott and his ministers are also furious about the episode being repeated, as is routine, albeit with Finlayson's statement appended.
Although the ABC is reviewing the decision-making processes that led to Mallah's appearance this week, the Government has announced its own inquiry into the offending episode. Abbott said the Government was "not satisfied with an internal ABC inquiry because so often we've seen virtual whitewashes".
The national broadcaster has also been under attack from the Murdoch press, with four News Corp tabloids running front pages on Wednesday featuring an image of a masked man waving an automatic weapon and a black Islamic State-style flag with the ABC logo Photoshopped on to it.
The controversy has also revived the long-running debate about free speech, with Peter Greste, the Australian Al Jazeera journalist released earlier this year after spending 400 days in an Egyptian prison, criticising the Government for "shooting the messenger".
"Anything that closes down debate, I think, is a bad thing, as long as the debate doesn't overstep the boundaries and become incitement," said Greste.
"I think we need to have vigorous debates, and I don't think that debate [on Q&A] crossed that line."
Addressing the Centre for Corporate Public Affairs in Sydney on Thursday, Scott said, "At times, free speech principles mean giving platforms to those with whom we fundamentally disagree."
In a reference to the French satirical magazine targeted by Islamic terrorists, he added: "It was the crux of the Charlie Hebdo argument last year ... Media organisations often give airtime to the criminal and the corrupt, to those who express views that run contrary to accepted public values.
"You have to set the bar very high before you begin to exclude certain views and perspectives."
Other ABC supporters noted that Mallah - who said on Q&A that Ciobo's comments "have just justified to many Australian Muslims in the community tonight to leave and go to Syria and join Isil [Islamic State]" - has been widely interviewed in the Australian media over the years.
Some also say he was making a valid point about the risk that a government discourse vilifying Muslims will radicalise young men.
The Australian, which often espouses the cause of free speech, appeared to mock that cause yesterday when it reported Scott's speech on its website under the headline "Je suis Zaky".
Earlier this week, Abbott demanded of the ABC: "Whose side are you on?" Scott said it was "clearly on the side of Australia", adding: "I hope no one seriously wants the ABC to be a state broadcaster ... [communicating] the messages of the Government."
The ABC has said it will co-operate with the Government's inquiry, which will report next Tuesday.
Its switchboard operators have described some of the calls received this week as "abusive" and "explicit".
The Communications Minister, Malcolm Turnbull, said: "I think it's very important that we get an understanding of the reason this judgement call [to have Mallah in the audience] was made, which was, clearly, as the ABC has acknowledged, so mistaken."
