McGuire, who suggested on Melbourne radio that Swans superstar Adam Goodes could be used to help promote a King Kong musical, has since held a press conference stating his comments were a slip of the tongue.
But the comments have deeply hurt Goodes and have stunned the Swans, with chairman Richard Colless stating bluntly a media personality of McGuire's standing should know better.
"I think a slip of the tongue is one word mispronounced," Swans chairman Colless told a packed press conference at the SCG.
Read the AFL's full statement
"This was actually a few sentences.
"I think having said it, he very quickly realised how inappropriate it was.
"I'd like to give Eddie the benefit of the doubt that it was an absolute slip of the tongue, but he's not a novice in this sort of stuff.
"He's been doing it professionally for 20 years and that's why I guess we'll remain bewildered.
"It was a very ham-fisted comment that really you would've thought only an amateur, who hadn't read the papers over the weekend, would make."
The Swans' main concern is for Goodes, who has been deeply hurt yet again, just five days after he was racially vilified by a member of the crowd in the game against Collingwood last Friday night.
McGuire was commended for his stance that night, but Colless feels much of that work has been undone.
"Friday, we believe in many years time people will look back and see it was almost a seminal moment in the bridging of the divide between black and white," Colless said.
"White Australians must understand there are things that cause grievous emotional pain to indigenous Australians.
"And we think in a way a lot of that's been undone five days later."
Colless, who said he believes Goodes has accepted McGuire's apology, revealed he had actually made first contact with the Collingwood president on Wednesday morning.
"He rang me following a text from me to him," Colless said.
"I just said 'I think we need to talk urgently. You know what I'm talking about. This is a very serious matter'.
"As Eddie always does he got back very quickly and I opened the discussion by saying 'what were you thinking?'
"He asked me whether I'd heard the tape and I said no but I've read the transcript.
"He felt that didn't give you the full story and you needed to listen to the tape.
"I'm not a radio expert but I thought the transcript was pretty explicit and I just said 'I just don't think you've got anywhere to go on this'.
"How can we defend a comment as crass as the one that you've made?
"He went to great lengths to explain the context and his physical tiredness and so on and so forth.
"As a club, it's impossible to underestimate how disappointed we are given who the individual is and given the highly commendable role that he played on Friday in providing support to Adam.
"The word that we came up with earlier was bewildered. We don't get it."
Colless said he doesn't believe the incident will hurt relations between the two AFL clubs in future.
James Dampney is a reporter for AFL.com.au. Follow him on Twitter: @AFL_JD