Jef (not Jeff) was not ever a GUI fan (either before or after the Mac). The Mac profoundly reflects a lot of his philosophy, but that philosophy was “a computer for the rest of us” (not his slogan, but Apple marketing’s): an appliance that was easy to use for “ordinary people”.
But he didn’t see the GUI/WIMP interface as part of that vision.
I would not say I am really well versed in his work, but the Zooming Interface Paradigm was what really stuck in my head from The Humane Interface and these canvas based UIs discussed in the article seem to be pretty much this.
Of course something like the Canon Cat takes an entirely different direction, but then I am also not sure that the line between GUI and Console Interfaces should be drawn this sharply. I think there are many examples were they blur together and can augment each other instead of being opposing concepts.
In general we still suffer from two terrible conventions from the 80s: the choice of application-centric silos rather than the document-centric model, and the bias towards the mouse (which was really a sop to fearful baby boomers) only recently partial broken by the iphone interface.