You can disable replication by repadmin
http://blog.scottlowe.org/2006/08/02/disabling-ad-replication/
But the better option is you can seize the FSMO roles on 2003 DC & run dcpromo /forceremoval to remove the AD from windows 2000 DC.
Remove the entry from dns as well as msdcs folder inside dns.
http://www.petri.co.il/delete_failed_dcs_from_ad.htmUpdate schema & configure 2008 DC.