I’m on the side that says it does work. Reading the writing of both spells, PWK kills any target below 100 HP. Polymorph transforms a creature into another and reverts only once the creature’s HP hits 0 or dies. Seeing as the spell instantly kills the creature, the creature polymorphed or not is the same. The polymorphed creature would revert but remain dead. Given the context, important creatures or characters ran in campaigns are relatively strong. They would have legendary resistances, magic resistances, or high save bonuses. Spell casters could even have counterspells; having said that, I wouldn’t worry too much about it. If ever it happens, it makes a funny or cool story to retell.