You probably want to explode your list of page ID’s using the explode function.
Something like;
<?php
$exmenuitems = explode(",",get_option('exmenuitems'));
$recentPosts = new WP_Query();
$recentPosts->query (array (
'post__not_in' => $exmenuitems,
'post_type' => 'page',
'showposts' => $menuitems
));
I’d recommend using the WordPress Menu building functions and admin interface. Its much more intuitive for end users to build their navigation menus via drag n drop that using page ID’s.