in WP 2.5, trunk, wp-admin/update.php, things start like this:
if ( !current_user_can('edit_plugins') )
wp_die('<p>'.__('You do not have sufficient permissions to update plugins for this blog.').'</p>');
I've disabled the edit_plugins, edit_themes and edit_files capabilities from my administrator role. I do the same for each of my customers, because I don't want them to see scary looking "Edit [File]" screens in their admin area. I'm guessing others do the same. Anyway...
Could it be possible to change the above to:
if ( !( current_user_can('edit_plugins') || current_user_can('administrator') ) )
wp_die('<p>'.__('You do not have sufficient permissions to update plugins for this blog.').'</p>');
And/or, change the message on the plugins screen as necessary, so that only relevant users get prompted to upgrade their plugins automatically? (i.e. change "There is a new version of [Plugin] available. Download version [X] here or upgrade automatically." to "There is a new version of [Plugin] available. Download version [X] here.")