Anyway, you can delete them either via API (e.g. using nxshell or custom java app) or by modifying database directly. I'd recommend API.

Something like this (do not run as-is, just an example):

for node in [o for o in session.allObjects if isinstance(o, objects.Node)]:
    c = session.openDataCollectionConfiguration()
    try:
        items_to_remove = []
        for item in c.items:
            if item.name == 'System.CPU.Usage':
                items_to_remove.append(item.id)

        for item_id in items_to_remove:
            c.deleteObject(item_id)

        if len(items_to_remove) > 0:
            c.commit()
    finally:
        c.close()