The idea would work. I am trying to stay away from solutions where thermal cycling of the peltier elements occur. It reduces the life span of the TECs.

PWM is the way to go. Since it can control the power much more fluently, even though in the microscale it switches on and off at kHz speed.
Either I use the motherboard, or I create my own potentiometer+thermistor controlled PWM circuit. Or rather I copy/modify someone elses.