Unfortunately no, as the isolation switch on top of the battery terminal, will cut off all electrical power to your vehicle.
If your car is fitted with one of these Thatcham approved alarms, then there has to be an electrical source supplying power to it.
You have probably discovered the only disadvantage to a cut off switch, but what's use of an alarm, if your up a mountain miles away from your vehicle, and someone is trying to steal your motor.
It would be far better to foil a thief, who simply cannot understand why your battery appears flat.
If he cannot start your vehicle, he will simply give up.