Afaik the X11 standard says that this shouldn't be done and that workspaces should span all monitors (or something along the lines of that), thus most DEs don't do this (I've read this in the gnome issue tracker), don't ask me why cause I also hate this behaviour. Most window managers will do that however and luckily it's super easy to replace xfwm with another window manager. I use i3 inside xfce on my work laptop, this guide describes how to set it up with ease
That's sort of how herbstluftwm models it. Workspaces are called tags, and are areas windows can be arranged. Monitors are like SVG viewports, with dimensions; Herbst auto-manages physical monitors, but lets you define virtual monitors with arbitrary dimensions. Workspaces (tags) are displayed on monitors and windows are adjusted to the dimensions of the monitors as tags are moved around. Monitors can be overlayed... the terminology is counterintuitive (windows have tags, but can only have one tag at a time, and monitors can overlap, etc), but it's a really nice way of approaching things IMO, and is one of the main reasons I'm sticking with X.
Do you mean you want separate sets of workspaces on each monitor and to be able to switch through them independently? Just having "workspace 1 on monitor 1 and workspace 2 on monitor 2" sounds no different than the default behaviour with no extra workspaces.
Gnome 3 has an option to keep one display fixed when changing workspaces... Also most window managers allow you to keep certain windows on all workspaces, maybe that will help?
KISS: Plug workstation 1 into monitor 1 and workstation 2 into monitor 2. Then use something like Synergy to share the keyboard and mouse between the computers.