"They were put in awkward situations because they had two contracts, and one would have been put in jeopardy if the other one was adhered to," Cheika said.
"It really put them in personal distress.
"Yes, we could play hardball but where is the bonus for me to cost Liam Gill his contract?
"If he really wants to go that much and doesn't want to play for Australia so be it."
But Cheika declared that this is no precedent decision, and no other players will be given early releases.
"It won't happen again," Cheika said.
"Guys have been put in awkward positions by their management. When I spoke to Toulon about Gill they didn't know he was contracted until December 31.
"Maybe the agents haven't taken the ARU seriously.
"One of these guys was saying that if it doesn't happen he's going to take legal action against us. I don't know where they get off.
"It's only that we're being nice people that they are able to fulfil those [overseas contracts].
"We've tried to do the right thing in this instance, we don't want them to have personal life grief because of it."
ARU general manager of high performance, Ben Whitaker, said the agent accreditation board insist agents must not induce a breach by a player of the "standard player contract".
"It is disappointing to be put in a position to make a decision when players have signed two contracts within the same term by their agents," Whitaker said.
"Therefore we really have no other choice but to release the players, as they have been put in a difficult situation where they have been mislead and misrepresented.
"If a contract runs until 31 December and any agent gets a player to sign a contract which commences on 1 August, he is forcing his client to breach his standard player contract.
"There's a responsibility that agents represent the best interest of their clients, however any breach of player agent regulations is putting players at risks of fines and sanctions, which is of great concern for the game."
But eyebrows were raised when ARU boss Bill Pulver openly met with Jarryd Hayne's agent Wayne Beavis, who is not accredited by the Rugby Union Players' Association, while other players have also done deals with unaccredited agents.
"Today's announcement by the ARU is the result of many weeks of ongoing dialogue and RUPA appreciates the ARU's concern for the players' best interests in coming to this decision," RUPA chief executive Ross Xenos said.
"We also appreciate the ARU's ongoing commitment to and support of the Australian Rugby Player Agent Accreditation Scheme. In recent times we might have questioned this commitment, but today's announcement certainly draws a clear line in the sand for all stakeholders."