There’s a huge amount to unpack beyond how I’ve put it, and I’m not well-versed enough to do it justice, but the issue is more around having a sex worker be the one who’s raped, and the sheer WTFfery of how they were going to “empower” her in the moment. And the additional details @DaveWallace posted which I’d forgotten about.
Ultimately, the issue with Whedon seems to be a lot of small things rather than one big thing. Like he’s not a terrible person, but he’s not as good as his press usually suggests. For a lot of people who are angry at the portrayal of minorities and women in the media, the championing of a creator like Whedon as if he represents feminism is almost a slap in the face - because of stories like this, or the Black Widow subplot in Age of Ultron where he suggests her infertility is a punishment for her shady past.
Now bear in mind I like most of Whedon’s work - but thinking that because he’s good at positive representation of women in some ways doesn’t mean he’s some feminist paean. And you could argue that the people who want him the hell away from Batgirl are overracting, sure. I don’t necesarily agree with them but that’s partially because I don’t give a shit about a Batgirl movie, and I’m not the one who’s feeling put down by the dodgy elements in his work. But you’ve got to take a look at some of the more nuanced criticism of Whedon’s work before deciding.