Spoiler
My thinking is that he didn't actually shoot the ghoul(s) in the well, only fired some shots to scare them off, and the 'thud' was not the dropping of a dead body but the sound of the wooden lid returning back to its place.
Yes, I was just about to quote the part about the doctor who brings up the matter of Pickman's face and speech degenerating into something less than human. Perhaps ghouls begin life very similar in appearance to human babies, but over time slowly change into their true form, aided by a diet of corpses, and Pickman made his disappearance just before he was no longer capable of disguising the change. The fact that his ancestors are very likely witches and comments were made on the close association between witches and ghouls in his paintings, is a fair suggestion to me that his whole family is in on it.
Yes, I was just about to quote the part about the doctor who brings up the matter of Pickman's face and speech degenerating into something less than human. Perhaps ghouls begin life very similar in appearance to human babies, but over time slowly change into their true form, aided by a diet of corpses, and Pickman made his disappearance just before he was no longer capable of disguising the change. The fact that his ancestors are very likely witches and comments were made on the close association between witches and ghouls in his paintings, is a fair suggestion to me that his whole family is in on it.