If you only need to move heat in one direction, you could use a standard switching controller in constant current mode and use the thermistor to trim the set point, either directly or via MCU. Look at external-switch LED driver ICs, some have an external setpoint input that can be used to control current without having to fiddle with the current feedback.
Or, since you don't necessarily need closed loop control of the current, you could implement your temperature PID or whatever in an MCU and drive a half-bridge power stage directly via PWM. As long as you're getting adequate heat movement to keep the temperature in regulation and your power stage doesn't cook itself you don't particularly have to care what the TEC drive current is. This also makes it easy to go full-bridge on the TEC if you need to provide heating as well.