Wiki page rank tanked after redirect to pretty URLs

I am admin for a site, which uses MediaWiki. We adjusted media wiki to use "pretty" URLs, this apparently screwed us over on SEO because technically its all redirects. We would have to revert it so /mainpage would go back to =mainpage.php? or whatever it was before pretty URLs.

Anyway, Google reports it as a redirect and will not index the site. Is there a way to get the site indexed and/or improve page rank?