My battery cable is completed fried/frayed/shredded. I called to get an estimate for a replacement and they told me the 2006 Sienna has a harness cable and I'd likely need to replace the whole harness. Have you ever heard of this and is it not possible to just splice the wire somewhere to repair?

Depends on what cable is fried, but splicing large cables carrying a lot of current is not usually a good idea unless it is unavoidable. Improper splicing and corrosion over time can cause resistance at the splice, and a voltage drop over a splice can compromise operation of the car and cause the cable to overheat and become a fire hazard. However, if done properly and other wires in the harness are not damaged, it might be an option.