I'd consider finding a ribbon cable to run into the fridge for the thermocouple in the fridge. If you find a nice thin one you can avoid having the uC and power inside the fridge eliminating most of those problems. Though this would be a less aesthetically pleasing method. As for your broken arduinos it's possible to program them again most likely with something like the USBtinyisp, at least if you haven't fried the uC itself.
I've thought of several variations on this idea. The most feasible was to have all of the electronics contained inside a plastic box, and this would stick to the side of the fridge with magnets. I'd run a tiny 3-wire cable to the temp sensor, which would sit inside the fridge. It's not the most elegant solution, which is what I'm chasing.
I'll look into reprogramming them, but assuming the Arduino prototyping board is ok, I'm only replacing the ~$5 ATMega processors.
