If I understand the question correctly, you would like to be able to switch workspaces independently for each screen, so that for example the left screen could be on workspace 1 and the right screen on workspace 3. This is supported by some window managers, most notably XMonad, and I personally find it extremely convenient in a dual-head setup. Moreover, it's perfectly possible to integrate XMonad with GNOME without sacrificing usability.
On my home machine I currently have a much simpler setup, with the default window manager. I like to have a music player visible on one of the screens at all times, so I just pinned the player to the visible workplace in order to emulate a “separate workspace”. This doesn't really solve a problem, but might be helpful anyway.