Campaign Life Catholic made the comments last week while criticizing the governing Liberals' anti-bullying legislation, which they say contains some "radical" elements driven by gay activists.
Jack Fonseca said McGuinty is "not a very strong Catholic" and has no right to dictate what kind of Catholicism gets taught in religious schools.
Representatives from other faiths say they agree bullies must be stopped, but can't condone the bill's requirement that schools promote sexual tolerance through gay clubs, saying it's an affront to their family values.
McGuinty said he's not troubled by accusations that he's betraying his faith.
"You've got to do what you think is right," he said Monday.
"Maybe different people bring different perspectives to that and different definitions. I have my own particular approach to this and it is the one that is informing our Accepting Schools legislation."
McGuinty was promoting the bill at Dr. G.W. Williams Secondary School, which is located just behind the constituency office of Progressive Conservative Frank Klees. Klees sponsored the Queen's Park news conference where religious groups criticized the sex ed component of the legislation.
Evangelican Christian Charles McVety accused McGuinty of using the problem of bullying to advance his "radical sex education agenda."
Others, including Jewish and Muslim groups, say they also believe that parts of the anti-bullying bill aimed at making schools inclusive and tolerant of gay lifestyles are offensive to many families.
Some warned there would be a mass exodus of students unless the legislation is amended.
But McGuinty has refused to revamp the bill, saying all Catholic schools will be required to have a gay-straight alliance even though they won't have to use that name.
During his school visit on Monday, the premier showed off a rainbow-coloured bracelet that was given to him by the parents of Jamie Hubley, a bullied gay teen whose suicide touched a nerve across the country.
But the premier wouldn't say whether he was trying to send his critics a message by making an appearance at the Aurora school.
It's a fundamental desire shared by all parents that their children feel accepted, safe and supported in school, he said.
"I think that's something that transcends all our differences, including our faiths," he said.
The controversy over gay-straight clubs in schools has also touched off a longstanding debate about Ontario's publicly funded Catholic school system, whose leaders don't always agree with the government's directives.
But McGuinty said Monday he has no intention of creating a single public school system in the province, even if it were recommended as a cost-saving measure for his cash-strapped government.
Former economist Don Drummond, who was commissioned by the Liberals to draft a report on government services, wasn't forbidden from making that recommendation, McGuinty said.
"We did not speak to that, but even if he were to recommend that, that is not something that we would pursue," he said.
His priority is making sure Ontario students receive a good education, which will help the province compete in a global economy, McGuinty added.
Last year, the premier clashed with Catholic school leaders over a revamped sex-ed curriculum.
He withdrew the draft rules after some religious and conservative groups, led by McVety, said they were uncomfortable with kids in Grade 3 being taught about same-sex families and sexual orientation.
The sex-ed curriculum hasn't been re-introduced and the government has yet to set a date for its release.