robots.txt:
User-agent: *
disallow: /drupal/
Then you'll want to submit an index for mysite.com/article to Google. It sounds like you won't be able to use XML sitemap for this however.
That should be all you need to do what you need. Of course the obvious question (if I understand what you're doing) is why you're using custom php to serve up Drupal content from the same domain, and not just doing this in Drupal.