The 20-year-old McDonald was brutally dropped for the grand final, with the Swans coach naming Hayden McLean - who hasn't featured in the AFL since round eight - as his replacement.
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"It's never easy, I've been on the end of that conversation before," Longmire said.
"It's tough you know, it's not easy on him. He's a young player with a great future for us and we just felt for this game we needed a bit more flexibility that Hayden gave us."
Longmire said stalwart Sam Reid and winger Justin McInerney both proved their fitness at Thursday training, having been under injury clouds that threatened their grand final hopes.
Reid, with Luke Parker the only players remaining from Sydney's 2012 flag-winning team, was substituted out of the preliminary final because of a groin injury, while McInerney suffered a sprained ankle.
"McInerney and Sam Reid got through it pretty well so we expect them to be ready to play on Saturday," he said.
If Reid fails to play, McDonald could earn a reprieve with the West Australian named as an emergency along with Braeden Campbell, Harry Cunningham and Will Gould.
"It's tough to go out of the team at any time but particularly for a grand final," Longmire added about McDonald.
Many fans took to social media after news of McDonald's axing filtered through, to convey their shock and disappointment for the Swans star.
Swans urged to trust their process against unchanged Cats
Geelong have named an unchanged side, including Max Holmes despite the wingman being subbed out of their preliminary final due to a hamstring injury.
The Cats, on a 15-game winning streak, enter the MCG finale as warm favourites.
But Longmire said his Swans, who have won their past nine games in a row, must believe in their system to cause an upset
"Just believe in what you do, the system," Longmire said of the message to his players.
"It's about turning up and about execution on game day.
"Don't use your energy up too early, save your energy for game day, and turn up and do what you do.
"They (Geelong) finished two games (wins) clear at the end of the home-and-away season and had a great win last week so they are clearly a very strong team.
"They have been fantastic this year but we look forward to that challenge."
"It is a big game and we just have to make sure we back in what we do."
Both clubs are featuring in Friday's grand final parade, which will have a markedly different look to past years.
Instead of travelling in slow-moving open-top cars through Melbourne's central business district, players and coaches from both clubs will be paraded along the Yarra River in a cavalcade of boats.
They will then greet fans at Yarra Park, outside the MCG.
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