Do a finder search for Spotlight keyword tag:red (for example), and select all of the found files and right-click to reveal Tags… menu entry. Click behind the tag name(s), backspace to remove it, and press return. Those tags are now removed from the selected files.
You can search for multiple tags on files using a capitalized OR, AND conjunction:
(tag:red AND tag:"special tag name")
Any other approach will require programming with Objective-C, and a list of tags to remove in a specific directory hierarchy. I am not aware of any third-party product other than the Finder/Spotlight combination that can remove custom tags.