I think that Harry is too dismissive of ‘souls’. He didn't think that magic existed, but it did, and if the people who deal with magic also claim to deal with souls, then there might be something to that. The idea that every human has a soul that goes to an afterlife may be silly (and even Wizards don't act as if they really believe that), but when talking about ghosts, Horcruxes, or the Dementor's Kiss, there might be something real that Wizards mean by ‘soul’, and Harry should investigate that possibility.
If wizards has some type of magically generated "soul", this would be grounds to treat non-wizards as a soul-less subclass. This doesn't seem to be the direction MOR is going.
Update: This post has also been superseded - new comments belong in the latest thread.
The second thread has now also exceeded 500 comments, so after 42 chapters of MoR it's time for a new thread.
From the first thread: