If you’re running Windows Server 2003, and want to upgrade to Windows Server 2008 R2, Please note; as long as the computer is Windows Server 2003 Service Pack 2 (whether or not the R2 product key and CD2 have been installed), you can upgrade. And as you already know, running Windows Server 2003 SP1 is unsupported anyway.
From TechNet docs supported upgrade scenarios from Windows Server 2003 (SP2, R2) to Windows Server 2008 R2:
Datacenter => Datacenter
Enterprise => Enterprise, Datacenter
Standard => Standard, Enterprise