I have written a small article about how to convert the default WordPress Atom 0.3 feed to a full-featured Atom 1.0 feed, which validates properly. It's titled:
Design the perfect Atom feed for WordPress
Here are some notes:
I also provide some brief info about how to enhance your Atom feed with RSS extension modules. In this article, I implement the Creative Commons RSS 2.0 module, so that the feed can contain CC license info. This is an example and it's there just to show you how to implement RSS extensions to your Atom feed.
All modifications need to be done to the default
wp-atom.php file. Keep a backup first, so that you can revert back to the default 0.3 feed, but I am sure you will not. Most bots seem to prefer the Atom feed over the RSS one.
Keep in mind that this solution is not official and should be considered only as a hack.