since the rest of the system is probably shot, then I would just leave it in place.

In the op's defense, if it isn't going to run for a while, why spend money on a part that may go bad or die while you are working on the car.
If it only has to stop when being loaded on a trailer or dropped off the trailer, why not get it to just work good enough and then rip it all out when it is ready to be rebuilt.