Well, first, PHP should be interpreting that file, so (if it's designed well) it wouldn't display any html to your browser.  Second, in your template fragment, you can do something like this:
  order deny, allow
  deny from all
...if all the config files are in their own directory.  Or even:
  order deny, allow
  deny from all
I'm not so sure about this one, but I think it would work.