It took a few hours of digging but I found the boot options in Windows 7+ can be changed using the command-line tool BCDEdit.exe:

Code:
            System.Diagnostics.Process proc = new System.Diagnostics.Process();
            proc.EnableRaisingEvents=false;
            proc.StartInfo.FileName = "c:\\Windows\\System32\\bcdedit.exe /set quietboot 1";
            proc.Start();
Note that the MSConfig option "No GUI Boot" is referred to as "quietboot" with BCDEdit and the user must have admin rights to make any changes.