The description of the undead type already contradicts the necessity of destroying the undead, and there's an argument to be made that a character and his corpse become seperate upon death unless he becomes an intelligent undead. Specifically, if it doesn't have his thoughts or memories, or indeed any thoughts or memories, its not really him. Just an animate husk that looks like him and used to belong to him.
As far as I can see there are no rules that explicitly tie a soul to a mindless undead creature, only ambiguous implication.
It doesn't much matter though. There's already a solid argument for mindless undead being evil without mucking about with souls. Intelligent undead are already only as evil as the want to be. Though in most cases their creation is evil even without being explicitly stated as such.