Hate might be strong, but Alan Moore definitely doesn't like it. He doesn't think it's very good personally, but also he's stated he thinks he went "Too Far" by crippling Barbara.
@Alan Moore:
I've never really liked my story in The Killing Joke. I think it put far too much melodramatic weight upon a character that was never designed to carry it. It was too nasty, it was too physically violent. There were some good things about it, but in terms of my writing, it's not one of me favorite pieces.
And yeah, part of why he's upset is he worries he helped usher in like a "Dark Age" of comics where nobody's really being original and are making it "Dark and Gritty for the sake of Dark and Gritty"
@Alan Moore:
But, as I said, [Killing Joke and Watchmen were] meant to be something that would liberate comics. Instead, it became this massive stumbling block that comics can't even really seem to get around to this day. They've lost a lot of their original innocence, and they can't get that back. And, they're stuck, it seems, in this kind of depressive ghetto of grimness and psychosis. I'm not too proud of being the author of that regrettable trend.
As for the topic of "Exactly what did Joker do to Barbara"… No, he still didn't do that to her.
A little while ago, Grant Morrison, one of the most recent long-running writers of Batman did an interview where he mentioned that he interpreted the final page of Killing Joke as Batman snapping Joker's neck.
Naturally, this caused a debate which led to the artists copy of the original script written by Allan Moore being scanned in its entirety and put online to scrutinize.
Now, Alan Moore is ridiculously anal when it comes to his script writing, including details for the artist to get the mood of the scene right. For example, here's how he described a chunk of the interaction between Batman and Barbara in the Hospital:
@Killing Joke Script:
HER FACE IS FULL OF PANIC AND DESPERATE ANXIETY. MAYBE WE SEE THE BATMAN'S COLD LEATHER GLOVE RUB HER HAND IN A FAIRLY INEFFECTUAL ATTEMPT AT PROVIDING WARMTH AND COMFORT. SHE REACHES UP TO HIM DESPERATELY BUT DUE TO THE IMMOBILITY OF HER LEGS, SHE CAN'T SIT UP VERY FAR."
It was nowhere near required for him to describe this in that much detail. He didn't need to say exactly why Batman reached out to Barbara and the narration didn't specify that, but he wanted the artist to know full well exactly why Batman was reaching his hand out so he'd know that while drawing it.
The implication that Joker did someting THAT horrible to Barbara WOULD be in these parts of the script. He would have mentioned that to the artist so he knew exactly what context to draw those scenes in.
Now, here is the unedited experpts from the script for the relevant scenes:
[hide][Panel 5]
NOW IN THE FOREGROUND OVER TO THE LEFT WE CAN SEE THE TWO BRUISERS DRAGGING THE BLOODIED AND UNCONSCIOUS POLICE COMISSIONER OFF PANEL TOWARDS SOME UNKNOWN DESTINATION. BEYOND THAT, THE JOKER, STILL WITH HIS GLASS I ONE HAND AND HIS CAMERA VISIBLE IN PLAIN SIGHT, IS SQUATTING DOWN ON THE FLOOR TO TALK TO THE STILL JUST-CONCIOUS BARBARA AS SHE SPRAWLS TWITCHING HELPLESSLY AMONGST THE SHATTERED FRAGMENTS OF THE COFFEE TABLE, THE RUINS OF GORDON'S JOKER SCRAPBOOK AND ITS ACCESSORIES STREWN ALL ABOUT HER AS SHE LIES THERE IN A CONSIDERABLE POOL OF BLOOD, EYES HEAVY-LIDDED AND BRIMMING WITH TEARS OF PAIN, SWEAT TRICKLING DOWN HER BROW. AS HE CROUCHES TO SPEAK TO HER, THE JOKER SMILES.
JOKER: You know, it's such a shame you'll miss your father's DEBUT, Miss Gordon. Sadly, our VENUE wasn't BUILT with the DISABLED in mind.
JOKER: But don't WORRY… I'll take some SNAPSHOTS to REMIND him of YOU.
[Panel 6]
NOW WE HAVE A CLOSE UP OF BARBARA'S HEAD AND SHOULDERS LOOKING DOWN ON HER THROUG THE JOKER'S EYES AS HE CROUCHES BY HER. SHE LOOKS HALF DEAD, WITH THE COLD SWEAT TRCKLING DOWN HER FOREHEAD AND HER EYES HARDLY ABLE TO STAY OPEN. SHE LOOKS AS IF SHE'S UNABLE TO MOVE HER BODY MUCH BELOW THE SHOULDERS, LYING THERE MOTIONLESS AND COMPLETELY HELPLESS, STARING UP INTO THE EYES OF THE OFF-PANEL JOKER. ALL WE CAN SEE OF THE JOKER HERE IS ONE HAND WHICH ENTERS THE PANEL AND STARTS TO UNBUTTON THE VERY TOP OF BARBARA'S SHIRT. THERE'S NOTHING SHE CAN DO ABOUT IT. IT IS THE JOKER'S LEFT HAND.
(SMALL) BARBARA: Wuh…
(SMALL) BARBARA: Wuh... why... are you...
(SMALL) BARBARA: Duh... DOING this...?
PAGE 14
[Panel 7]
NOW A HEAD AND SHOULDERS SHOT OF THE JOKER, LOOKING UP AT HIM THROUGH BARBARA'S EYES AS HE CROUCHES OVER HER. HE SMILES AND LIFTS HIS GLASS TO HER IN A TOAST. CHRIST, HE LOOKS EVIL. THE GLASS IS IN HIS RIGHT HAND WHILE HIS OTHER HAND REACHES DOWN OUT OF THE PANEL TOWARDS US IN THE FOREGROUND.
JOKER: To prove a POINT.
JOKER: Here's to CRIME.
[…]
PAGE 17.
[Panel 1]
NOW WE MOVE OUT OF FLASHBACK AND CUT ABRUPTLY TO GOTHAM CITY HOSPITAL IN THE PRESENT. IT IS VERY EARLY IN THE MORNING, PROBABLY ONLY A LITTLE AFTER MIDNIGHT, AND WE ARE IN THE PRIVATE SIDE WARD CURRENTLY OCCUPIED BY BARBARA GORDON. WE ARE STANDING BY THE RIGHT HAND SIDE OF HER BED (AS LOOKED AT FROM THE FOOT OF THE BED), UP NEAR THE TOP SOMEWHERE AND JUST BEHIND THE BATMAN, WHO STANDS RIGHT NEXT TO THE BED, LOOKING DOWN AT IT. WE ARE AT HIS WAIST LEVEL OR THEREABOUTS, AND WHAT WE SEE OF HIM HERE, OVER ON THE EXTREME RIGHT AND FACING AWAY FROM US, IS JUST A LITTLE OF THE BACK OF HIS BLACK AND TRAILING CLOAK, AND MAYBE HIS BLACK-GLOVED HANDS. THE HANDS ARE HOLDING THE JOKER PLAYING CARD THAT WE SAW HIM EXAMINING THOUGHTFULLY EARLIER IN THE EVENING, BACK AT THE BATCAVE. LOOKING PAST HIM, OVER ON THE RIGHT OF THE FOREGROUND, WE CAN SEE PART OF THE BED AND WE CAN SEE BARBARA GORDON'S LOWER HALF, WHICH IS CLAD IN ONE OF THOSE SHORT, UGLY-COLORED HOSPITAL SMOCKS THAT COMES DOWN TO JUST ABOVE HER KNEES. SHE IS ON HER BACK AND HER UPPER HALF IS CONCELAED FROM US HERE BY THE BATMAN'S BACK, WHICH BLOCKS OUR LINE OF SIGHT. ALL WE CAN SEE ARE HER LEGS. ENTERING FROM THE LEFT OF THE PICTURE AND REACHING OVER THE BOTTOM OF THE BED WE SEE THE HANDS OF A DOCTOR, WITH STARCHED WHITE SLEEVES, AND MAYBE A BIT OF HIS CONCERNED AND SERIOUS LOOKING FACE, IF HE'S LEANING FORWARD FAR ENOUGH. HE HAS HIS HANDS UPON BARBARA'S ANKLES AND IS REARRANGING HER NERVELESS LEGS. THE VISUAL JUMP BETWEEN THE SRHIMP HAVING ITS LEGS PULLED OFF AND THE DOCTOR'S HANDS ON BARBARA'S USELESS LEGS IS INTENTIONAL, SO PLAY UP ANY INCIDENTAL SIMILARITIES IN THE VISUALS AS MUCH AS POSSIBLE.
[…]
LOOKING OVER BARBARA'S LEGS AND THE BED THEY ARE BEING ARRANGED ON WE SEE HARVEY BULLOCK, COMISSIONER GORDON'S UNDERLING FROM THE REGULAR BATMAN BOOK. THE MAN IS A SEAMY AND UNSHAVEN SLOB WITH A SECRET HIDDEN STREAK OF DECENCY, AND AS HE STANDS ON THE OTHER SIDE OF THE BED LISTENING TO THE DOCTOR'S VERDICT HE LIGHTS HIS STUBBY CIGAR WITH A PAINED AND DISGUSTED LOOK, ALMOST WINCING AS HE HEARS WHAT THE DOCTOR HAS TO SAY AND LOOKING AWAY IN SICK DISGUST AT THE THOUGHT OF ANYBODY CAPABLE OF DOING SUCH AN INCREDIBLY VILE THING TO A COMPLETELY INNOCENT YOUNG WOMAN. THE LIGHTING IN THE ROOM IS SUBDUED AND SHADOWY HOSPITAL NIGHT-LIGHTING, EXCEPT FOR THE SUDDEN FLARE OF A MATCH HERE AS BULLOCK LIGHTS HIS CIGAR.
DOCTOR: The bullet went through her SPINE. I'm afraid her LEGS are completely USELESS.
DOCTOR: Putting it Bluntly, she may well be in a CHAIR for the remainder of her LIFE.
[Panel 3]
NOW WE ARE LOOKING DOWN ON THE HOSPITAL BED FROM UP NEAR THE CEILING, SO THAT WE CAN SEE BARBARA FULL FIGURE AS SHE LIES THERE ON HER BACK, EYES CLOSED. BULLOCK, SMOULDERING CIGAR IN ONE HAND, IS JUST WALKING SLOWLY AROUND THE FOOT OF THE BED TOWARDS THE SIDE WHERE BATMAN IS STILL, STANDING IN THE SAME POSITION LOOKING DOWN AT THE STILL FIGURE IN THE BED, STILL HOLDING THE PLAYING CARD IN ONE BLACK GLOVED HAND, WHICH IS HANGING DOWN BY THE SIDE NEAREST TO US HERE. BULLOCK SEEMS TO GLANCE ACROSS AT THE CAPED FIGURE WITH A WORRIED LOOK. IF WE HAVE ROOM TO SHOW THE DOCTOR, HAVING COVERED BARBARA UP HE IS PREPPING TO LEAVE THE ROOM, JUST WANDERING AWAY OFF PANEL IN THE DIRECTION OF THE DOOR, WHEREVER THAT HAPPENS TO BE.
BULLOCK: They didn't TELL you?
BULLOCK: He'd removed her CLOTHING after SHOOTING her. we, uh…
BULLOCK: Well, we found a LENS-CAP on the floor that didn't fit any camera in the place. We believe that, uhh...
[Panel 4]
NOW WE HAVE A HEAD AND SHOULDER FULL FACIAL CLOSE UP OF THE BATMAN. HE HASN'T MOVED… HE JUST STARES OUT OF THE PANEL AT US WITH HIS BLANK WHITE EYES AND THE EXPRESSION ON HIS FACE IS UTTERLY COLD AND UNREADABLE. LOOKING OVER HIS SHOULDER WE CAN SEE BULLOCK, WHO IS STILL CIRCLING THE ROOM AND IS NOW OVER BEHIND THE IMMOBILE BATMAN. HE IS LOOKING AWAY FROM BOTH US AND BATMAN, AND HIS FLABBY UNSHAVEN FACE IS IN SHADOW HERE.
BULLOCK: Well, that he took some PICTURES.
BULLOCK: Of her.
BULLOCK: Jeez, look, really, I'm SORRY. I thought you KNEW. It's pretty SICK ain't it?
[/hide]
At NO Point in ANY of these scenes does Moore elaborate at all on what was done to Barbara or even INFER to the artist that he should consider anything else having been done to her. It's stated she was shot, it's stated he undressed her and took photos, and the story treats those two things alone like the sick depraved acts they are.
With his scripting, Moore would have mentioned something, inferred something to the artist if he meant him to even imply what people say happened here. Obviously, if Moore wanted to imply that, he has to make sure the artist knows the intent when he draws each panel. Yet his direction includes NO reference to sexual assault whatsoever.
Simply put, it didn't happen. Just like how Batman doesn't break Joker's neck in the end. Some people just decided to read it that way.