If you are sure it is just theft, and not vandelizm, then the locked area should be okay. But, if they are smart, and it is left unattended for a long time, a set of bolt cutters will get them in.
There are a lot of ways to disable a vehicle, but there are a lot of small things that can be stolen from it as well. In addtion, if they are drunk or get pissed off, they can do a lot of damage as well.
If you just want to disable it, take an expensive part that is needed to start the car. If it is an old jeep, then that makes it harder to do, so I would consider some hidden kill switches. For instance, one under the carpet that gives you power in the start postion, a momentary would be best here. Then an on/off for power while in run.
If it is a newer jeep with efi, then take out the fuses and relays for the fuel pump, and maybe even remove the coil packs.
Also consider an alarm to the local pd if that is a possiblity.