for refrence if anyone finds this via search I found some functions to enable and disable plugins
function activate_plugin($blog_id, $plugin) {
if (empty($plugin)) return;
if (validate_file($plugin)) return;
if (!file_exists(ABSPATH . PLUGINDIR . '/' . $plugin)) return;
switch_to_blog($blog_id);
$current = get_option('active_plugins');
ob_start();
include_once(ABSPATH . PLUGINDIR . '/' . $plugin);
$current[] = $plugin;
sort($current);
update_option('active_plugins', $current);
do_action('activate_' . $plugin);
$res = ob_get_clean();
if (!empty($res)) echo "Error activating $plugin for blog id=$blog_id: $res<br />";
restore_current_blog();
}
function deactivate_plugin($blog_id, $plugin) {
if (empty($plugin)) return;
if (validate_file($plugin)) return;
if (!file_exists(ABSPATH . PLUGINDIR . '/' . $plugin)) return;
switch_to_blog($blog_id);
$current = get_option('active_plugins');
array_splice($current, array_search($plugin, $current), 1 ); // Array-fu!
update_option('active_plugins', $current);
ob_start();
do_action('deactivate_'.$plugin);
$res = ob_get_clean();
if (!empty($res)) echo "Error deactivating $plugin for blog id=$blog_id: $res<br />";
restore_current_blog();
}
It takes the blog id for the blog you want to do it on and the relative path to the plugin file from the plugins directory.