Yeah, proportional control -- PWM into an LC filter is preferred. If you need bidirectional operation, use an H-bridge directly*, or a controlled current (PWM into LC) into an H-bridge (that's only switched occasionally, to toggle polarity). I did one of these some years ago, for a dewpoint control, for a major paint-mixer machine supplier (of all things!).
*In which case, treat each leg as its own PWM output, LC filter each. Why? If you leave one side pegged to a switching node, you get the full switching noise on all the wiring. NFG!
Or, switch the one side only occasionally, set PWM on the other side to D or 1-D depending on polarity, and use just the one LC -- this still lets through full switching noise when changing polarity, but that's probably not very often, so is acceptable. Note the LC filter also doesn't track instantly (it's referenced to GND), so there's a upset when changing direction. This would suck for most applications (e.g. mains inverter, class D audio amp; maybe motor driver), but doesn't really do anything to the TEC, it's just getting blasted with whatever charge was in the cap.
This probably doesn't make much sense without a diagram, but eh that's okay, if you want to know more just ask.
Tim