In theory it should work - in both cases you would install a Windows 2000 without the upgrade to SBS2000. Regarding the licensing issue - I would recommend the safe way and call Microsoft about this. I can only guess, but I would expect that they say that this is not allowed.
The SBS 2003 license is a new one or an upgrade license of the SBS 2000 version?
To fix the issue with your other Windows 2000 CD that won't format the harddisk I would recommend to try to create a new CD with newer/updated storage driver and possibly slipstream Service Pack 4 for Windows 2000 into it by using
nLite - Deployment Tool for Unattended Windows.