When the setup gets to the part where you are asked to name it, simply hit SHIFT-F10

you'll get a command prompt.

Type "control system" and press enter

use the system control panel that pops up to change the workgroup name but leave the server name and everything else alone.

close the window, don't reboot the system. Continue with the setup, and once it's all going you'll have that workgroup name and the certificates in certificate services will be named properly too