You should be able to do this with the same filter that is talked about here.
The full-size images are being kept by WordPress. It’s not really a WooCommerce thing. As well as the settings for images in WooCommerce you will also need to set minimum image size in WordPress’s Settings>Media...
Then this script (see the link above for complete discussion) should remove the originals.
add_filter( 'wp_generate_attachment_metadata', 'delete_fullsize_image' );
function delete_fullsize_image( $metadata )
{
$upload_dir = wp_upload_dir();
$full_image_path = trailingslashit( $upload_dir['basedir'] ) . $metadata['file'];
$deleted = unlink( $full_image_path );
return $metadata;
}