Thompson, a three-time premiership player with Essendon and dual flag-winning coach of Geelong, was convicted for drug possession in 2019.
He was fined $3000 and ordered to undergo rehabilitation, while a drug trafficking charge against him was dismissed.
Separately, Thompson was fined $30,000 for his part in the Bombers' infamous 2012 supplements program.
The 59-year-old, who left the AFL after coaching Essendon through the 2014 season, has worked to rebuild his life in recent years away from football.
He will present the McHale Medal to the premiership coach on stage after the grand final at the MCG on September 30.
"In our game, I think people make mistakes and I think we have an ability to actually welcome people back and continue to celebrate their place and their role in the game," McLachlan said.
"That is certainly where Mark is. He was a great player and a significant coach, and I'm really pleased that he's going to be presenting the (medal) to the premiership coach.
"I hope it's significant for Mark and I think it's significant for the game."
Thompson was confirmed as this year's McHale Medal presenter at the official AFL finals launch on Monday.
"I think he's pleased," McLachlan said.
"I think Mark needs to speak to that for himself but I do think it's significant."
Former Carlton and West Coast champion Chris Judd will present the Norm Smith Medal on grand final day, while former Sydney Swans captain Josh Kennedy is this year's premiership cup ambassador.
The AFL also confirmed American rock band KISS will headline the grand final pre-game entertainment show.
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