Have the key fob beep or buzz when it gets used, along with a panic button that the user could hit on the fob to force the car off and set off the alarm. To defeat against the attacker cuts off the amplifier just after getting the car started, have the car shut off if it loses contact with the key fob within the first 15 seconds.

Edit: just thought of another possibility -- use spread spectrum. An amplifier would have to be tuned to a specific frequency. With spread spectrum, the car and key fob switches frequencies every second based on a cryptographic function, therefore defeating the amplifier.