Use whatever version of Windows necessary (use Windows 3.1 if you need to) but keep it offline and connect it directly to your Linux / BSD workstation via serial (or ethernet).
Then glue that old PC to the actual hardware you use and treat it like a bit of extended firmware (or Lights Off Manager).
Then you can SSH, RDP, VNC to interact with the old hardware through the old Windows and use it in a safe and secure manner.
Quite a lot of scanners and printers are going this route these days too.