If I am understanding the problem, maybe what you should do is to choose a window manager that can disable a given binding when the focus is at a given window (blender, in this case). I think fvwm can do this, but it takes some learning to use it with proficiency.
In any case, there will always be shortcomings to this. While you are working at blender you will surely sometimes activate that key combo hoping for the blender functionality, but sometimes you will forget you are working with it and hence you will expect that combo to take you to another desktop. The only real solution is mind-reading, which computer will handle someday, but not quite yet. In the while, what I suggest you is to use saner bindings. In a pc the mod4/win key does nothing useful, if you become accustomed to use it for all your WM bindings there will not be conflicts with most applications, probably. That's what I do. Learning some WMs can be time consuming, but configuring the keybindings is usually quick enough. -- Jesús Guerrero Botella
