You could easily hack the thing to provide the feed you want to provide. Look at this bit of code:
switch ($feed) {
case 'atom':
require(ABSPATH . 'wp-atom.php');
break;
case 'rdf':
require(ABSPATH . 'wp-rdf.php');
break;
case 'rss':
require(ABSPATH . 'wp-rss.php');
break;
case 'rss2':
require(ABSPATH . 'wp-rss2.php');
break;
case 'comments-rss2':
require(ABSPATH . 'wp-commentsrss2.php');
break;
}
It's fairly obvious how that works. Just change the first three to use wp-rss2.php instead of what they are currently using. Don't mess with the comments one, it handles feeds for your comments on individual posts..
Note that this isn't exactly safe, some aggregators may not like you switching formats from what they were expecting like that. But I think most will handle it okay.
You may also want to look in your theme's header.php file, and remove the lines at the top which advertise your other feeds. They will look similar to this:
<link rel="alternate" type="application/rss+xml" title="<?php bloginfo('name'); ?> RSS Feed" href="<?php bloginfo('rss2_url'); ?>" />
Just delete the ones for ATOM and RSS1, if they are there, and leave the RSS2 one.