Hello,
I was searching for a different answer when I ran across your question. I don’t know if this is what you’re looking for a or not, and I don’t know what the SEO plugin did/did not do for you, but this is the code that I use to exclude my pages. It’s in my header editor:
<?php echo preg_replace('@\<li([^>]*)>\<a([^>]*)>(.*?)\<\/a>@i', '<li$1><a$2><span>$3</span></a>', wp_list_pages('echo=0&orderby=name&exclude=1,2,3&title_li=&depth=1')); ?>"
Just replace ‘1,2,3’ with whatever the page ID#’s are.
I hope that helps.