"(I)t amounts to requiring a Catholic institution to speak about Catholicism in terms defined by the state rather than by its own understanding of Catholicism," the court continued.
The decision protected parents' rights to transmit the Catholic faith to their children and to guide their religious upbringing.
School boards in Alberta have until the end of March to approve their policies implementing the guidelines. Eggen, the education minister, said there would soon be meetings with Catholic Church leaders about the guidelines.
Bishop Henry's stance has drawn objections from critics such as University of Calgary professor Tonya Callaghan, who is monitoring what she considers to be homophobia in Catholic schools. She told CBC News that the Catholic Church's position is "discriminatory, oppressive and should be abolished."
According to her faculty profile page, her research aims to "free members of sexual and gender minority groups from religiously-inspired heterosexist oppression."
Bishop Henry countered criticisms that the Catholic view is judgemental.
"Only God can judge the state of the human soul but it is pure nonsense to suggest we cannot and should not judge human behavior. Reluctance to judge moral behavior is the inevitable consequence of moral relativism and moral subjectivism that has eroded confidence in the ability to determine objective moral truth on which sound judgment is based," he said.
He noted that Pope Francis spoke about gender ideology in his 2015 encyclical on care for our common home, Laudato si'.
"The acceptance of our bodies as God's gift is vital for welcoming and accepting the entire world as a gift from the Father and our common home," the Pope wrote.
The Pope noted the need to accept one's body in its masculinity or femininity.
"In this way we can joyfully accept the specific gifts of another man or woman, the work of God the Creator, and find mutual enrichment. It is not a healthy attitude which would seek to cancel out sexual difference because it no longer knows how to confront it," Pope Francis said.
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