At the request of the artist, DC Comics have pulled a cover for a forthcoming issue of the Batgirl comic after a storm of protest from fans.

The cover, by Rafael Albuquerque, was a “variant” cover to the forthcoming issue 41 of the fan-favourite comic, and depicted the heroine with tears in her eyes and with Batman villain The Joker dangling a gun over her shoulder and drawing a blood-red grin across her face with his finger.

It was meant as a homage to 1988’s seminal Batman standalone story The Killing Joke, written by Alan Moore, in which the Joker attacked – and probably sexually assaulted or raped – Batgirl aka Barbara Gordon, daughter of Commissioner Gordon, leaving her in a wheelchair.

Batgirl #41’s original cover artwork, which will now be the only one on sale. Photograph: DC Comics

June has been designated “Joker month” by the publisher and all its comics will be available with an alternative cover option featuring the clown-like villain in some form.

Angry fans took to Twitter with the hashtag #ChangeTheCover exhorting DC comics to pull the Batgirl variant, which the series’ regular artist Cameron Stewart later revealed had not been run past the creative team of writer Brenden Fletcher and artists Babs Tarr and Stewart. Batgirl has been one of DC’s biggest hits in recent months, thanks to its light and fun tone. Along with Marvel Comics’ Captain Marvel and Ms Marvel, Batgirl has been highlighted as one of the titles responsible for getting more women reading comics.

Teresa Justino, writing on the female-centric comics website The Mary Sue, said: “It’s disturbing. And while it’s certainly drawn well, and it references a classic story from The Joker’s history, the fact is, it’s not what many of Batgirl readers of any gender want to see for one of DC’s few female heroes currently with her own title.”

However, a counter-movement sprang up, with others calling on DC to #SaveTheCover – among them American actor Adam Baldwin – and saying that pulling the cover would amount to censorship.

On 16 March, DC Comics released a statement saying that the Albuquerque cover was now not going to run – at the artist’s request – and said that there had been “threats of violence and harassment” over the cover:

“We publish comic books about the greatest heroes in the world, and the most evil villains imaginable. The Joker variant covers for June are in recognition of the 75th anniversary of the Joker. Regardless if fans like Rafael Albuquerque’s homage to Alan Moore’s The Killing Joke graphic novel from 25 years ago, or find it inconsistent with the current tonality of the Batgirl books - threats of violence and harassment are wrong and have no place in comics or society. We stand by our creative talent, and per Rafael’s request, DC Comics will not publish the Batgirl variant.”

Reference point … Batman: the Killing Joke comic book from 1988, written by Alan Moore. Photograph: DC Comics

Albuquerque himself said: “My Batgirl variant cover artwork was designed to pay homage to a comic that I really admire, and I know is a favourite of many readers. The Killing Joke is part of Batgirl’s canon and artistically, I couldn’t avoid portraying the traumatic relationship between Barbara Gordon and the Joker.

“For me, it was just a creepy cover that brought up something from the character’s past that I was able to interpret artistically. But it has become clear, that for others, it touched a very important nerve. I respect these opinions and, despite whether the discussion is right or wrong, no opinion should be discredited.

“My intention was never to hurt or upset anyone through my art. For that reason, I have recommended to DC that the variant cover be pulled. I’m incredibly pleased that DC Comics is listening to my concerns and will not be publishing the cover art in June as previously announced.”

Batgirl’s regular artist, Cameron Stewart, took to Twitter to clarify DC’s statement and said harassment hadn’t been directed at Albuquerque personally, but to people objecting to the cover. He added in a series of tweets: “I stand behind Rafael as an artist and a friend, and think he made the right decision. The cover was not seen or approved by anyone on Team Batgirl and was completely at odds with what we are doing with the comic. So, we have the creators of the book and the artist himself all agreeing that the cover was inappropriate. There’s no ‘censorship’ here.”

Further fuel to the fire was added today as people began linking to reports of a 2006 interview Alan Moore gave to the comics magazine Wizard in which he recounted the editorial decision to allow The Joker to injure Batgirl to the point of disability. Moore is reported as saying he was told by his editor: “Yeah, okay, cripple the bitch.” The comment later gave its name to a website which “explores sexism in the geek community”.

It isn’t the first time an apology has been issued around Batgirl in recent months; in December the creative team issued a statement acknowledging the “hurt and offence” their depiction of a transgender supervillain might have caused.