Drupal and long-polling/sockets
Yes, implementing comet/long polling in Drupal is a bad idea.

There already is a node.js project that you could use: Drupal node.js integration.

The design principle of that module is that node.js does not contain any logic (to avoid duplication of logic in PHP and JS) but is only reponsible for keeping a connection open to your users. You then send notifications to node.js in the usual hooks (like hook_node_save()) which forwards it to your users.