The Scot declared the affair "embarrassing" and vowed to "deal" with the issue, with his defender being one of several Premier League stars to boycott wearing the T-shirts before their games.
Manchester United legend Viv Anderson has said that Ferdinand was wrong in his approach but the players' union chief, Clarke Carlisle, believes that the former Leeds and West Ham man has every right to his beliefs and that they should be respected by his club.
"We will definitely monitor the situation very closely and make sure Rio Ferdinand's rights as a human being, never mind as a footballer, are not undermined in this position," he told BBC Radio 5 Live.
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"And then for all these players to get together and put what it is they want down on paper so we together as a union - all the players, one with another - can make those changes and move forward.
"There are two sides to this one," Carlisle continued.
"First of all, Sir Alex Ferguson is continual in his unwavering support for the Kick It Out campaign, which is commendable and what we all want to see, but you can't vilify or coerce any individual for making a stand.
"This shouldn't be seen as an element of control or defiance - just like Sir Alex Ferguson said when he was talking about [fellow boycotter] Jason Roberts in his first interview, he doesn't know the reasons why this stand is being made and what we should do first of all is hear those reasons and listen to them and take them on board.
"Sir Alex Ferguson said he was embarrassed and that is because of the statement he had made but Brian McDermott and Alan Pardew, these guys said they had entered into dialogue with their players and listened to the reasons for them making their stand.
"So I would sincerely hope that Sir Alex Ferguson now speaks with Rio Ferdinand and asks him why he wanted to make that stand and hopefully supports the position he is in and it isn't seen as a player-against-manager situation."