Martin Samuel told the Sunday Supplement that Sir Alex Ferguson should accept Rio Ferdinand's stance over the Kick It Out campaign.
The Manchester United defender refused to wear a T-shirt in support of the anti-racism movement ahead of Saturday's game with Stoke, despite his manager insisting on Friday that all of the club's players would do so.
Speaking after the match, Ferguson said he was disappointed by his player's act of defiance and insisted: "He's let us down, so we will deal with it."
But Daily Mail journalist Samuel insists Ferguson should be more open to Ferdinand's rights to express himself as he sees fit.
"It's not helpful language to say he will be 'dealt with'," he told the Sunday Supplement.
"There's more of a conversation that needs to be had and maybe more of a conversation needed to be had before this.
"Alex has obviously got his opinion, which is that everybody should wear these shirts, there should be a unity and we should all be seen to be going in the same direction, which I can understand.
"But he's got to accept there will be people who do not agree with that; Joleon Lescott hasn't worn a Kick It Out T-shirt since 2007.
"Within that you've got to allow freedom of expression. This is about freedom of expression."
Reading striker Jason Roberts explained earlier this week that he would not wear the T-shirt because he didn't feel enough was being done to combat racism in English football.
He referred to incidents in the last year, including the case involving John Terry who was banned for four matches for racially abusing Rio's brother Anton Ferdinand.
Samuel believes players have a fundamental right to protest and questioned if Ferguson was simply concerned by Ferdinand's actions because it implied a lack of managerial control
"I don't necessarily agree with what Rio did, but I would defend his right to do it," Samuel said.
"The T-shirt is a statement, I've always thought it was gesture politics, and if Rio doesn't want any part of it then that's his right.
"I couldn't understand Sir Alex on Friday being so adamant that he would wear it when it was quite common knowledge that there were these grave misgivings about it.
"Alex coming out on Friday saying 'he will wear it' sort of boxed himself into a corner and set up an inevitable clash with Rio.
"Rio is his own man on this, as he's perfectly entitled to be, and he made the decision not to wear his T-shirt.
"I can understand Alex Ferguson saying he feels embarrassed because it makes him look as if he hasn't got control of his players and he puts great store by being able to be the guy that's in charge.
"That makes him look weak."