There seems to be some confusion as to whether PWM damages Peltier elements. If that is your only concern, go ahead and use PWM.
Here is a scientific approach to the question. The paper's conclusion is that the damage done over thousands of hours of operation is small and not significant.
However, this site points out that with regard to power input, PWM makes less efficient use of available power. Again, if power cost is not a concern, go ahead and use PWM.