The Sinn Fein member said he was bitterly disappointed and saddened, at both a political and personal level, that the institutions created by the Good Friday agreement had been suspended.
"They held out great hope and promise. I believe that, despite the limited time we had, we had begun to realise this potential. We had made a good start in addressing some of the major policy and strategic issues in the education of our children."
Mr McGuinness, who was minister for only nine weeks, set out a long list of objectives including reducing class sizes and completing the review of the curriculum to promote excellence, provide choice, enhance access and ensure quality.
He appealed to the direct rule minister, George Howarth "to adopt and develop all these points so that the political vacuum which is causing so much frustration, does not also paralyse the development of better, more democratic and more equitable approaches to the provision of education."
In his firmest statement yet on a key issue facing Northern Irish education, he told the conference "I believe passionately that the selective transfer system at age 11 is unfair and should be replaced."
This view was endorsed by Social Democratic and Labour party assembly member Patricia Lewsley. Delegates later reaffirmed the ending of selection as union policy.
But Danny Kennedy, the Ulster Unionist who chaired the assembly's education committee, made clear that comprehensive education would not sail through. "Until I see what is recommended to replace the present process I am going to reserve judgment."
Des Rainey, the national president of the all-Ireland union, said that the obsession of Government with testing and assessment had imposed an adult concept of learning on primary schools and robbed children of their childhood. He claimed the pilot system of baseline assessment was "an educational absurdity" which must be abandoned.
He also urged the churches to take up the challenges of the Good Friday agreement by considering sharing the management of mixed schools.
Delegates, alarmed at the "tidal wave" of violence and disruption, were determined to reduce teacher workload and get extra cash for education. In this they echoed delegates at the National Association of Schoolmasters Union of Women Teachers conference the previous weekend.