Well if your goal is to get the cpu as cold as possible to achieve a higher clock speed, Then adjusting the amount of current going to a tec is not the way to go. But if you want to run just enough power to the tec to allow the cpu run just under ambient temp to prevent any problems with condensation it would make sense. Personally I would rather get the cpu as cold as the tec will allow and make sure you seal everything up good so you have no worries.
I do remember reading an article about a piece of hardware that allowed you to controll the power of the tec. I'll see if I can find it for ya. That is if were thinking of the same thing?