If you follow the above directions it would behave as if certificate services was never installed. The question is if you use the certificates for anything besides workstation enrollment, e.g. internal web site certificates, smartcard logon, email signing/encryption, EFS, IPSec, etc. If you do, then you will want to migrate it, if not and you have no real plans to, then you can just uninstall as described to get rid of cert svcs and remove it properly from AD.
If you plan to continue using your own certs, then you will need to open up the Certification Authority MMC and do a full backup of the CA - bear with me its been awhile since I've driven a w2k CA, but it should be similar to 2k3 if memory serves:
right click the CAName - All Tasks - Backup CA
In the wizard make sure to select to backup the Private key and CA Certificate, the Certificate database and certificate database log. Do not do an incremental backup. Browse to the save location (note: must be an empty folder). Assign a password for the private key - make this strong and do not lose it.
Build up a new virtual server at the same OS and service pack level, restore the CA there and then upgrade to 2003.
The guide is here:
How to move a CA to another server:
http://support.microsoft.com/kb/298138
