When you have a page that's still on the site (even though it's removed from navigation), the page is still on the site and indexed--so users will still get to it. It's still probably going to rank for at least something in the search results.
What you need to do is figure out if the page still contains valid content and is useful for visitors. There's obviously a reason that the page was requested to be removed by the content manager, though.
If the page needs to be removed from navigation, and it won't have any internal links, then most likely you probably need to remove the page, as well. What I would do is set up a 301 Permanent Redirect from that URL to another on-topic page on the site. As long as you use a 301 redirect and redirect it to another internal page on the same domain, you won't lose and "SEO value".