I wonder if exploits like this might encourage the use of fanless computers in these ultra-secure locations? There are quite a few processors on the market now which give decent performance without the need for a fan.
Perhaps a cheaper way to solve this is to hide the physical case inside a locked cabinet, with a ventilation fan? Most users of secure systems don't need physical access to the case, and the ventilator should drown out any signal noise from such malware.
You can always do something like spread-spectrum modulation of the transmitted signal to recover it from below the noise floor.
Perhaps a solution would be to design a CPU where every instruction consumes exactly the same ammount of power.