Farrell has chosen to miss the Six Nations, which starts in February, "in order to prioritise his and his family's mental wellbeing".
The shock decision comes after Farell led England to a third-place finish at the recent World Cup, his side losing to eventual champions South Africa in the semi-finals.
Farrell, who has long been a divisive figure for some rugby fans, was sent off in a warm-up game against Wales, which resulted in a four-match ban, meaning he missed England's opening two fixtures at the tournament in France.
He came under fire on social media and at times was booed by sections of the crowd during the World Cup.
McCall said he was impressed with Farrell's performances in light of the criticism he was facing - the fly-half became England's all-time record points scorer in France.
"It's remarkable that he played the way he played during the World Cup, if we take into account how he was feeling," said the Saracens boss.
"He is a person who is right on top of his game at the moment, yet he and his family have been made to feel the way they feel. It is shameful. It's not right," he said.
"I've worked with Owen for 15 years, every day, and the person that has been portrayed in the media bears no resemblance to the person I know. He's a family man, they've always come first.
"There was a narrative created and started and that's been there for quite some time. There's only so much that someone can take."
World Rugby chairman Bill Beaumont, himself a former England captain, said he hopes Farrell can return to international rugby "reinvigorated".
"You don't ever want to live in a society where somebody like Owen Farrell, who has been a great servant to rugby, should be booed when he's playing for his country," Beaumont told the BBC.
"It's very disappointing for him and his family and he obviously feels he needs a break away from the spotlight of the international game to recharge his batteries and come back."
England begin their Six Nations campaign away to Italy on February 3.
