McIlroy and US Open runner-up Shane Lowry opted not to compete for Ireland due to fears over the Zika virus, which has links to defects in newborn babies.
"The shame for Rory is I really think he would have benefited from being around other athletes," McGinley said.
With Graeme McDowell also absent, Padraig Harrington and world number 291 Seamus Power will represent Ireland.
Three-time major winner Harrington, 44, and wife Caroline, who have two children, plan to watch as many other sports as possible in Rio after the golf tournament is over.
"It's really good for the heart and the soul to be involved with so many other athletes where it's the most important thing in their game," said McGinley, who captained Europe to Ryder Cup victory over the United States at Gleneagles in 2014.
"I think Padraig is going to come back a better person for it and the Irish team are going to benefit a lot from having Padraig around.
"The Olympics will really stand them in good stead when they come away and back into the golfing environment again, having experienced other sports and seeing how other people approach it and also bouncing ideas off trainers and all kinds of experts who are going to be down there.
"To be part of the biggest sporting event in the world is an opportunity that I'm certainly looking forward to."
World number four McIlroy 27, has spoken about his desire to start a family in the near future, saying: "My health and my family's health comes before everything else.
"Even though the risk of infection from the Zika virus is considered low, it is a risk nonetheless and a risk I am unwilling to take."
Golf is returning to the Olympics after a 112-year absence but three of the world's top four players - Jason Day, Dustin Johnson and McIlroy - plus major winners including Adam Scott and Louis Oosthuizen have chosen not to play.
The Olympics take place from 5 to 21 August.
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Ireland's Olympic golf captain Paul McGinley says Rory McIlroy could have learned from playing in the Rio Games.