As described above, don't do it. From what I understand, some / most of the windows updates should work. What won't work are big changes like a service pack. That will hose your CCM (or Unity.) Not worth it. And there is no way to know which patch will work and which one will hose your system.
Security agent will (should--ok, has been) good at denying bad things from getting through. So If you can't get to performing a set of patches, you should be relatively "Safe".
As for the OS being non-standard or whatever, it's just a "locked down" version of windows. Local Policy changes, maybe a couple programs deleted, services stopped, etc. You can't uninstall much from a Windows Install without MS doing it for you and they aren't going to do it for you.
I hear there is a third-party (non IPT related) appliance that has a stripped down Windows 2003 that Microsoft created special for them. I don't have the details on what was left out.
