Hi Peter,
Right now that is not something the average user can configure via the settings, but if you are willing to get your hands just a little bit dirty, it is not very hard.
Next, launch AppleScript Editor (if using Snow Leopard), or Script Editor (on Leopard and below).
Right click on the installer on your desktop. and select Show Package Contents from the contextual menu (or whatever the equivalent in Path Finder is). Then within that find Contents/Resources/Tag Folders.app and drag it onto AppleScript Editor's icon in the dock.
Once the script is open, scroll down until you find a line that says
on manageLinks(thefiletofind)
Below that you will see a block of code that ends with the line
end manageLinks
Select all the text in between those two lines (do not include the two lines themselves). Then right click on the text to bring up the contextual menu, and select Comment Tags. This will add a (* at the beginning and a *) at the end of your selection. Save the changes and quit AppleScript Editor.
Close the window showing you the contents of the installer app package. Now run the installer. It will update all your existing Tag Folders with the modified script. Ta-da! Your Tag Folders will no longer create Smart Folders in ~/Library/Saved Searches.