I brought up this issue with a wiki admin on a wiki I edit from time to time. This person was able to use the Exists template (http://meta.wikimedia.org/wiki/Template:Exists) to solve the issue. Pages that are searched for with the Exists template solution only do NOT show up on the wanted pages anymore! However, pages that are linked through actual red links elsewhere will still show up on the Wanted Pages, which is exactly what we want.
The pages that have actual red links will still show the #ifexists as a wanted link on the Wanted Pages (so a page that had a missing link and an #ifexist call would show (2) pages that link to it) because the #ifexists call will show up on the "What Links Here" for any page, with a "(transclusion)" beside it.
I've asked the admin to post the solution here, to help others with the issue.