I'm not an expert on ODB2 but you can use a core with any vehicle. You may not be able to use the ODB2 interface with a non-supported vehicle.
I'm not sure that you'll be able to read any of the signals but you could always use the inputs on the Core and tap in to wires (i.e. park kill, etc.) and achieve the same function "the old fashion way".
EDIT: There's a facebook group called "The Whelen Command group". You could post this question there to see if anyone has tried a Wrangler before. I have not seen anyone post that they have but it doesn't mean they haven't!