The former Three Lions boss expressed sympathy for the 64-year-old, following criticism over his decision to omit Rio Ferdinand whilst calling up John Terry for Euro 2012
The FC Twente boss, who previously endured a disasterous 16-month spell in charge of the national team, says Hodgson has done what he believes is best for the team in selecting John Terry over Rio Ferdinand.
Hodgson cited "footballing reasons" for Ferdinand's initial exclusion from the squad though it has been suggested that he was reluctant to include the 33-year-old alongside Terry, who is currently facing a charge for racially abusing his brother, Anton.
The Manchester United stopper even dismissed the former Baggies' boss' claims via Twitter this week, after a call-up was handed to inexperienced Liverpool defender Martin Kelly following Gary Cahill's withdrawal.
McClaren told Sky Sports News: "He [Hodgson] is in a lose-lose situation. He's made that decision. It's always going to be controversial but he has had to be strong and he has had to make it.
"[He's tried] to avoid the media circus that would go on and on and on. Imagine the media attention surrounding John Terry and Rio Ferdinand every day, at the hotel, stories coming out in training.
"I think what Roy has had to do is choose between the two of them; he's chosen John Terry. I'm sure in an ideal world, without all the controversy around, it he would take both.
"Rio is a fantastic player, he had a great season for Manchester United. John Terry is such a focal point for England as a team, as a squad, as a captain and as a leader."
The 51-year-old noted that it was crucial to avoid any disharmony within the squad, claiming it could damage England's chances of succeeding in Poland & Ukraine.
McClaren added: "The most important thing is when you are together for six weeks in a hotel and you are cocooned within that environment, if you've got anything going on within that squad that hampers the harmony and togetherness that has to be avoided."