The AFL is expected to soon sanction the club over last year's supplement program, having spent more than a week reviewing the Australian Sports Anti-Doping Authority's interim report into the saga.
There has been speculation that no specific anti-doping charges will be brought against players under the World Anti-Doping Agency (WADA) code, but the AFL could still heavily punish the Bombers under its own rules.
Matthews says it seems likely Essendon and its senior officials will be sanctioned for bringing the game into disrepute.
But he doubts that's the appropriate charge.
"We've had this leak and that leak and now we, as in the grapevine, seem to believe there'll be no specific rule breaches but the AFL will go back to its catch-all of bringing the game into disrepute to make a scapegoat of somebody," Matthews told Brisbane's 4BC radio on Monday.
"The somebody is the Essendon management, whether it's James Hird, the coach, or the club itself.
"But I am yet to see any evidence of what they have actually done to bring the game into disrepute, as opposed to innuendo that we read about in the paper day after day.
"... If you have to go back to bringing the game into disrepute what you're saying is 'Our rules aren't good enough.'
"In other words they haven't broken any specific rule, but we don't like what they've done so we'll slam them with bringing the game into disrepute."
Matthews said the AFL Commission, which will hand down any sanctions, had the right to act in the game's best interests as the code's governing authority.
"But I don't see anything that Essendon have done at this point in time that you could say they've brought the game into disrepute," he said.
"Yes, they may have been sloppy in their governance, sloppy in their management, they might have delegated to some people that they wish they hadn't delegated to potentially.
"But that isn't bringing the game into disrepute in my view.
"It's one thing to look after your brand and your game but you've got to make sure there's an element of fairness in what you eventually do."