When you are running Windows in either Parallels or booting your Mac into Windows using Boot Camp, there should be no functional difference from running Windows on generic PC hardware.
Your Mac *is* a PC. There are no major differences at a hardware level. So, the differentiating factor is the operating system. When you run Windows, it's not in emulation.
With that said, if you can't just pop in the disc, open it from "My Computer" and start the installation, then the disc is faulty.
Most companies that do volume licensing with Microsoft are also eligible for Microsoft's "Home Use Program". With the HUP, you can purchase a copy of Windows for your own use for $20 (both Mac and Windows versions are available). For that $20, you get a properly licensed and commercial disc that is supported by MS. I would recommend you check with your company's IT department to see if they have the needed contact information to order such a copy.