She's more of a weird in-between for me. Without the Joker she theoretically could have been a good person (until AU started showing up where she's still psycho anyway) she still had/has a working conscience, sanity and the rest of it. It's just all overpowered by her love for the Joker and the resultant insanity. I like the fact that in BTAS she is almost entirely lucid as to just how fucked up everything is.
When written well, her madness is more subdued for lack of a better word. She's only the tiniest bit past the line. She doesn't realize her henchmen are dead because she can't handle their death so she hallucinates them, when released from arkham she fails to notice social cues (aka Running around with hyenas on rollerskates is frowned upon and immediately jumps to the conclusion that she's being accused of theft when a security guard comes to get rid of her tag), and so forth.
The nature of her evil (love, which is never considered negative and is a noble goal in the eyes of) combined with the fact that she's not as blatantly in your face psychotic as the rest of the bat gallery makes it easy for people with bad analysis skills to mistake her as better than she actually is.
I mean really, idiots think the joker is some paragon of truth. Is it so hard to see how it's easier for Harley to get a similar treatment?