Is there any reason why you can't just mount additional forum packages for each department? You could do that dynamically using the site_node Tcl API. Of course it depends on how many departments we're talking about, I have no idea how it'd scale on a larger scale.
What you're describing actually sounds a lot like dotLRN to me, which solves the problem by mounting a subsite for each department. Depending on the scope of the system you're building, there's always the option of using and perhaps extending dotLRN to some degree. Maybe total overkill, not sure :)
