Plugin Commander will do the auto-activation, but if you want an automatically activated plugin to have certain settings different from the defaults, you will either need to modify the plugin or build a separate plugin having this framework:
function blog_defaults( $blog_id ) {
// the following examples set core WPMU options
add_option('blogdescription', "Yet another My Site blog");
add_option('permalink_structure',"/%post_id%/");
add_option('posts_per_page','25');
add_option('template', 'mytheme');
add_option('stylesheet', 'mytheme');
add_option('current_theme', 'MyTheme');
// the following examples set plugin options
add_option("wpcms_post_control_revisions","n");
add_option("wpcms_post_control_autosave","n");
return;
}
add_action('populate_options', 'blog_defaults');
There are existing plugins that set core WPMU options but none to my knowledge that set plugin options.