I have had the same problem, solution was to put in a Honeywell Perfect Climate system. It allows two thermostats and averages the temperature, plus it offers a bunch of other options such as running the fan 20 minutes out of every hour, all the set back stuff, humidity and ventilator controls etc.
I think they still sell them at:
http://customer.honeywell.com/techlit/PDF/50-0000s/50-8151.pdf
Easy wiring....a unit goes next to your furnace, it uses the existing 4 low voltage wires to run the head unit, I think it is just two wires to the remote temperature sensor.
It has a neat outdoor temperature feature that varies the humidity based on outside air temperature so you don't get frost on the windows, plus it monitors the run time on the fan and reminds you to replace the filter when needed.
Good system...I have two...
Dennis