The facts of what happened seem rather unclear.
According to this interview from 2007 she did know about the rape scene beforehand, it just wasn't in the script & she felt pressured into doing it:
"That scene wasn't in the original script. The truth is it was Marlon who came up with the idea," she says.
"They only told me about it before we had to film the scene and I was so angry.
"I should have called my agent or had my lawyer come to the set because you can't force someone to do something that isn't in the script, but at the time, I didn't know that.
Also, the article in the link you posted says all the sex was simulated.
Clearly wrong & callous to pressure her into doing scene she wasn't comfortable with, but people seem to be interpreting it to mean that she was actually raped on set; not sure this is the case.