You can simply deactivate any NextGEN gallery plugin from the Plugins menu of your administration panel before automatically upgrading WordPress. Once you’ve completed your upgrade, just go back to the Plugins menu and activate NextGEN. It shouldn’t affect how your site runs, and the plugin should come right back with no problem.
The NextGEN series of plugins create beautiful photo galleries for your website that are easy to manage and include a lot of features for your blog.
When trying to upgrade WordPress to 3.0 on one of our client’s sites, we discovered that it took us to an error page located at /wp-admin/update-core.php with the text “You are not allowed to call this page directly.”
This thread details the problem and the fix.
Future versions of WordPress and NextGEN may address this auto-update problem in the future.