In an oral history of the enduring 1996 teen witch film posted by EW, casting director Pam Dixon reveals that Jolie was just one of several up-and-coming actresses who auditioned for the part of Bonnie, the leader of the high school coven who was eventually played by Neve Campbell. Dixon recalled:
"[Neve] was by far the biggest name [because of her show Party of Five]. We tested Alicia Silverstone, Scarlett Johansson, Angelina Jolie, but Neve came in and she was really, really good."
At the time, Jolie was just three years into her professional film career and had starred in her first Hollywood picture, Hackers, in 1995. She was also two years away from her first big breakthrough in the 1998 HBO biopic Gia, so conceivably The Craft might have accelerated her path to stardom. With her dark demeanor she certainly would have fit right into the movie (of course, she got to play a witch years later in Maleficent).
As for Johansson, she was just 11 or 12 at the time and probably too young although she was acting already, while Silverstone had starred in the hit Clueless in 1995 and was arguably the biggest theatrical star at the time to audition for the movie.
The full article is worth a read for all you Craft fans out there, who have provided the film with a healthy cult following for the past two decades. The snarkiest part of the piece occurs when the subject of the witchy TV series Charmed comes up. The Craft star Robin Tunney puts it point blank:
“Charmed is a rip-off of The Craft. It was completely obvious to the point that people would think I was on Charmed for years after.”
And she just might have been, had Angelina Jolie taken one of the lead roles in the movie instead. How do you think The Craft would have turned out with the now megastar Jolie as Bonnie instead of Neve? Or do you think the cast of The Craft was perfect just as it was? Who knows, perhaps there's a role for Jolie in the proposed sequel?