Hi Ben,

Let's see if you've already tried the easy solution first. The portal page for the wiki folder (the top page in the folder) has options for hiding unwanted web parts. For the labkey.org docs, you can see the close boxes I've circled in the attached screen shot.
  
Closing these web parts will eliminate the search and TOC web parts from all wiki pages in the folder, for all users.

Will this work for you?

Thanks,
Elizabeth