I've spent the last year and a half playing with temperature control processes and temperature probes for cookers. The reason why companies don't use thermocouples is that they are too darned expensive. Thermistors can be bought with pennies. Thermocouples normally have platnum in them so even the cheapest made thermocouples are still expensive.
The next reason is the controllers. The cheap oven probes that use thermistors don't require much on the electronics side; they're basically just ohmeters that convert resistance to temperature. Just like the probes, thermocouple controllers are more complex and therefore are more expensive.
If you are bent on useing thermocouples though, thermoworks has a pretty decent thermocouple controller for less than $45.http://www.thermoworks.com/products/handheld/mtc.html
I use their plug type thermapen and am very happy.
I also use Phidgets USB thermocouple controllers to connect to my control system on my laptop.
Keep us updated on you PID controller project.