Add a filter for post_type_link
, and change its value in a callback function.
Sample code, not tested:
add_filter( 'post_type_link', 'simple_woo_urls', 10, 2 );
function simple_woo_urls( $url, $post )
{
if ( 'product' === $post->post_type )
return home_url( $post->post_name );
return $url;
}