If they can fix it so that Barbara Gordon is not such a victim, great, but it's not like they're going to remove the fact she gets paralyzed from the story, is it? The problem is central to the story, I think the moment they decided to reimagine it as an animated movie, they made a choice to perpetuate that stereotype.
Is it really central, though? The Joker's goal isn't to cripple Barbara; his goal is to drive Jim Gordon insane. His assault on Barbara is merely a tool toward that end. The significance of TKJ to Barbara herself was something that wasn't established until a totally separate set of stories many years later, and the movie won't be adapting those stories. What the Joker did to her was not about her; it was about Jim. It's more a Macguffin than anything else. That's exactly the problem with it, in fact -- that this powerful, independent, well-loved heroine is reduced to merely a pawn of a conflict between two male characters, and that her life was changed forever because of a story that was not actually about her in any way.
Let's break it down.
The Killing Joke is a 48-page graphic novel -- 46 if you disregard the opening and closing pages that are just an image of a puddle in the rain. Barbara Gordon appears on only six pages and is mentioned a single time each on two more. She only has dialogue on three pages, one of which gives her only one sentence. Her last appearance in anything other than photographs is on page 19, less than halfway through. Looking through the GN for the first time in a while, I can really see exactly why it's seen as such an awful, marginalizing treatment of the character.
So really, you could probably cut Barbara out of the story entirely and it would have little impact, as long as you could come up with a substitute way for the Joker to torment Jim in the funhouse. Say, maybe footage of the Joker killing innocent Gothamites. Barbara is nothing in TKJ but a means to an end, so one could substitute a different means to the same end without losing any of the core of the story.
But -- there is another option. Like I said, the story's only 48 pages. That's about half the length of
Batman: Year One. The B:YO adaptation was extremely faithful, with hardly anything cut out and a couple of bits even added. So if we assume TKJ is meant to be a 70-odd-minute movie like the others, they'd probably have to add content to fill the running time. We already know they're adding a 15-minute prologue to set up the story. There's still room to add another 20 minutes of content, perhaps.
So what they could do to fix the Barbara situation is to add a subplot that's about her, that gives her agency and a point of view in a way the comic failed to do. Maybe that's part of the goal of the prologue; maybe we'll see her as Batgirl helping to capture the Joker, and his attack on her would be retaliation for that. And maybe later, we could see added scenes showing her coping with her paralysis and considering how to move on -- perhaps hinting at the possibility of her becoming Oracle, although it'd be hard to do that in the brief time frame of the story.
Either approach would help: either remove her from the story altogether, or include her fully in the story as a core character with an inner life rather than treating her simply as an appendage or a prop. Both would be better ways of handling Barbara while allowing the core narrative involving Batman, the Joker, and Jim Gordon to remain intact.