I can only think of one Giles-as-villain story off the top of my head, though surely there are more out there! I don't think this is exactly the kind of thing you had in mind - it's an alternate universe fic, not a story where you see Giles go "bad", and he's really only present in the story for a few paragraphs, but he makes quite an impression. When She Was Bad, by Julie Fortune. (Unlike 99% of the fic I recommend, this is not Spuffy. It's S3 era gen fic.)