The symfony2 standard way is to have a copy of all js and css files in your web directory. Think of it as a clean separation between user/client accessed files and strict server side files. You can workaround it, but you shouldn't.
To solve your problem, after each update to your server you have to delete all files in web/resources/bundles (to make sure removed files from your bundle are not present anymore) and rerun
php app/console assets:install web