The ARU is investigating a verbal altercation between Beale and Wallabies business manager Di Patston during a flight from South Africa to South America on Sunday.
McKenzie, though, says he and his three assistant coaches merely couldn't find room for the troubled star on a bench containing six forwards and only two backs for a match they expect to be extremely physical.
Beale had little impact after going on early in the second half of Australia's 28-10 loss to South Africa last Saturday, a match in which the Wallabies led 10-8 entering the final 10 minutes.
McKenzie has preferred the more abrasive Rob Horne as backline cover for the late stages against the rugged Pumas.
"We think it's going to be fairly physical and we want to have strong defensive finish to the end of the game," McKenzie said.
"So we concentrated on that around selections and that's where we are."
McKenzie and lock James Horwill said the mood remained positive in the Australian camp despite the swirling controversies and a difficult build-up.
"Players, they're footballers in the end and their job is to play football," McKenzie said.
"So the best thing they can do in terms of contributing is to do exactly that."
