I usually include a chunk in the <header> part of all my website templates to control how i wish the search engine’s to treat my content. Maybe it is also a suitable alternative for your website.
When developing i put this in my chunk:
<meta name="robots" content="noindex,nofollow,noarchive" />
When the site is finished and filled with content i change it to:
<meta name="robots" content="index,follow" />
I once had the same situation as you have and i kept the old website which started with index.html which seems to get a higher priority then index.php on apache based webservers. Beside changing the meta tag i then additionally deleted this index.html file and made the other old files html redirect to the new website’s root.
I have not read any clear comment from a reliable source on how many/which search engines support this tag but from what I experienced at least google seems to respect it.