Nelson Rockefeller was actually the one that commissioned Diego Rivera for the piece. The article makes it sound like John D. Rockefeller was involved with the commission. Nelson like his mother was a big patron of the arts. The story I have heard was that Nelson was interested in having it moved to MOMA(Museum of Modern Art) and paying for it. For some context Nelson's mother was Abby Aldrich one of the founders of MOMA. The sculpture garden at MOMA today is named after her. Given their interest in the arts and being involved in that circle in Manhattan it seems rather unlikely that Nelson would have ordered it to be destroyed. Although it certainly makes for a more exciting narrative - class struggle, art and violence. Why the move of the piece to MOMA never happened seems be lost to the dustbin of history unfortunately but I have heard it posited that Diego felt the destruction of it was of greater value as a political statement.