How can I change a smart folder's icon without changing the default icon?
How can you change the colors of the glyphs in the Finder sidebar, while leaving them as their default icon? You can't (unless there's a third party tool about which I am unfamiliar). However, you can change the default icons to your heart's content. Here's how:

As a test, I created a Smart Folder that finds all PDFs in my home directory. The default glyph for the Smart Folder is a gear, as noted in the OP.

Here are the steps to change the glyph:


Locate the directory /System/Library/CoreServices/CoreTypes.bundle/Contents/Resources
Locate the file called SidebarSmartFolder.icns





Rename it to SidebarSmartFolder_old.icns
Paste into Resources folder the glyph you want to use in its place.
Rename it to SidebarSmartFolder.icns
Reboot your Mac.


You'll see now that my Smart Folder glyph in the sidebar has changed to the new one.