Driving a Peltier w/ PWM or analog out
Perhaps I over simplify but how about using a mosfet transistor or similar with a thermal resistor that "chokes" the current when desired temperature is reached, that way it will alter cooling seamlessly depending on thermal load and the peltier should be happy to work like that. If calibrated right I believe it may also eliminate any over current problems if your power source is bigger than your load. Good luck in your project.