It's somewhat tricky.
Dynamic Punch has far more damage, and a much better Damage per Energy than Power-Up Punch. PuP has low energy cost, so you can at least use it often.
If you have Counter, I *think* it's fine to give up Dynamic Punch for PuP. Ice punch is pretty necessary coverage for Medicham. The other feasible option would be to run Psycho Cut in the Fast Move, and then Dynamic Punch/Power-Up Punch. I do that with my Poliwrath (but with Bubble instead of Psycho Cut). Poliwrath's Rock Smash is weak so he can't really rely on it as much.
So yeah, you can probably swap it off if you have Counter.