Gregory says he is non-religious and has chosen to opt his son out of religious observance in school - which parents have the right to do.
Gregory said he had concerns that school chaplains were "preaching" to children and said schools should include more diverse representation, for example, by inviting atheists along as well.
He said: "Obviously, at school there is religious and moral education, which is fine; I think that is important and a fundamental part of knowing about religion.
"But the other side is religious observation where people come in, usually Protestant chaplains, to preach to children.
"My wee boy came home telling me a story he had overheard about falling in rivers and good Christians saving them.
"I felt they were trying to imply that you had to be Christian to be moral. You don't need the church to teach morals and you don't have to be religious."
A parent quoted in the ESS report said she had attended school assemblies at her son's primary school, which were led by a minister from the local Protestant church.
She said: "At these assemblies the minister brings a Bible with him which he holds in his hand and talks to the pupils about the 'special book'.
"He gives a sermon then asks the pupils to pray. This is not a few moments of 'silent reflection'.
"The minister leads the prayer in the manner he would in a church setting, expressly praising, worshipping and appealing to the Christian God and Jesus Christ."