It takes around 15 min for your dome lights to go off when a door is left open, or in this case, doors removed. There are 4 lights, usually. One on each side, down by your feet, as well as the two up top next to your speakers.
I would guess that your battery was a bit weak, and the lights being on for that much time either ran the battery down or, now I'm not sure if our Jeeps have this, but in some cars they have a voltage monitor, and if there is a constant drain, the system shuts down.
I've had this happen once when a friend pulled the key out but didn't turn the ignition off all the way. (my key can be pulled out even when driving).
Try unplugging the battery terminals, then re connecting them. That should solve your issue...hopefully.
03 TJ Rubicon