Get a plugin called Tekkit customizer. It can ban items from your world and there is an option where you can add id's to Banned World. It will DELETE ALL commandblocks once a player loads a chunk with the command blocks in. OR you could get World edit and do //removenear <radius> (id)

MCEdit them out, worldedit them out. You do not need to delete the world as that retard above me said.

just disable command blocks in the config then use a plugin to delete it from all loaded chunks it should work fine

MCEDIT

You can't without deleting the world.