I think that "liking" has a lot to do with it. I've also read a lot of bashing fics; and I understand both Giles' motives in-story (see my note to rebcake downthread), as well as the bashers' reasons; but it always makes for an unpleasant read. I did recently read a post-The Gift story (can't find the link) that initially seemed to be yet another story bashing Giles and the Scoobies (they're the worst, yadda yadda) to make Spike look good; but then eventually it evolves so that I understood that the writer was portraying the situation from Spike's POV as he and Giles come to a moment of shared understanding. Quite clever, actually.

Oh - just yesterday I read a story where Giles does something "necessary but horrible" - another AU take on The Gift, by desoto_hia873, "All Set Down" from 2005. Not a "Big Bad" fic, but quite good. I'd forgotten it when I wrote this.
http://desoto-hia873.livejournal.com/162450.html

And I have no idea why there aren't more Evil Anya fics. Maybe because for most of the run her role is a comedic one, and the one episode that does deal with her past seriously is also the one that made me cry when the sword was run through her, in which she was willing to sacrifice her own life to make right what she'd done wrong? (And was willing to make that sacrifice as a demon, btw. Just sayin'.)