You have to remove the system somewhere in the wiring the system either opens a circuit or grounds it to disable the van. You must pin point that circuit so that it can be repaired if it's a circuit that is opened by this device. If it works just by grounding the circuit (and many do) simplely removing the devices wiring should disable it. Make sure you remove all of it many devices have a couple of seperate boxes.
The first thing to do is follow the wiring back from the card swiper and start carfully re moving the wires repairing insulation and rejoining any wires that may be cut. Use a single edge razor blade to cut away any electrical tape thats in the way.
I would disconect the battery be for starting this project.