To be fair, he had his spinal cord bruised and compressed. Some people have recovered nearly fully from injuries like that. (I believe Bruce was like 75% recovered already before his magical healing. He was walking, he just wasn't going to be running the rooftops anytime soon.)
Barbara had a portion of her spine blown away. In terms of medical science, there's no coming back from that.
Of course, it still makes no sense for Barbara to be in the wheelchair when Zatanna can just swoop in and say "enips s'arabrab laeH", but internal logic is always the first thing to go in a shared universe, amirite?