The main protagonists were the Rev Jack Laidlaw, a former education adviser in Tayside, who is convener of the Church's education committee and an outright opponent of Section 2A, and Ann Allen, a Glasgow teacher who is convener of the board of social responsibility and opposes "blanket repeal".
But both united to oppose the Government's proposed replacement wording in the Ethical Standards in Public Life Bill that local authorities should promote "stable family life" in their care and education of children. This was "a totally meaningless term which is offered as a sop to deflect the mounting concerns being expressed throughout Scotland", Mrs Allen said. It was "absolutely unacceptable".
The commissioners strongly backed their view that marriage - "the love that dares not speak its name," as Mrs Allen put it - should be emphasised as the norm for permanent heterosexual relationships and therefore as the appropriate environment in which to bring up children.
The Assembly's suggested new clause for the Bill reads: "It is the duty of a council in the performance of those of its functions which relate principally to children to have regard to the value of marriage, parental commitment and family relationships in a child's development".
But, despite the private referendum this week showing 86.8 per cent of Scots want to retain Section 2A on a 34 per cent turnout, ministers seemed adamant that the primacy of marriage would not be written into the legislation replacing it. The Executive has already conceded a statutory requirement that education authorities must heed national guidance on sex education.
Mr Laidlaw mounted a vigorous defence of repeal, arguing: "There was no evidence of worried people or anxious parents complaining that homosexuality was being promoted in Scottish classrooms before the clause was enacted in 1988 and there is still no evidence of that now the replacement is proposed."
Parents had been unnecessarily alarmed by scare stories that homosexuals were poised to flood schools with propaganda. "I am also perturbed that much of the discussion seems to infer that teachers are witless individuals who would happily prsent children with anything that came to hand," Mr Laidlaw said.
"We should acknowledge the professionalism of our teachers and be confident of the careful and responsible way that teaching about relationships and sexuality is approached in Scottish classrooms. I know of no one who wishes to promote homosexuality in schools.
"We need to ensure that children and young people can become informed, confident and responsible about their sexuality. For the majority, that means coming to terms with a heterosexual orientation, but for a small minority it means coming to terms with a homosexual orientation.
"All our children need to be accepted for who they are, encouraged and supported."
Mr Laidlaw reminded the Assembly that the board of social responsibility had urged it in 1994 to "deplore all prejudice against and maltreatment of people because of their sexual orientation."
Mrs Allen distanced herself from charges of homophobia and said homosexuals must be "valued, loved and pastored". But the drive for equality "should not mean that our culture and ethics in Scotland are moulded by the demands of the lifestyle of such a tiny minority of our population".
She added that a blanket repeal of the legislation banning the promotion of homosexuality in schools without any alternative protection could not be supported. "In their determination to embrace liberalism and inclusiveness, the Scottish Executive have, in my opinion, become entrenched in illiberalism and exclusiveness," Mrs Allen said.
The failure of the Scottish Executive to endorse marriage, she said, was at odds with the Green Paper issued last year by Jack Straw, the Home Secretary, who said that "marriage is the surest way for couples to bring up their children".
Marriage, she continued, "is important to Christian people and we are not going to see it sidelined to another alternative status".
The fears which have been kept alive by the "keep the clause" campaign surfaced briefly when the Rev Alastair Horne from Falkirk recalled watching a film with his children which had been given a 12 certificate. He had been shocked to watch a scene in which two men were kissing.
Mr Horne told the Assembly: "There are those groups who are promoting their views in many ways, many of them in your face . . . they are actively promoting a lifestyle that the Bible does not."