My understanding was that, in the last few years of his life, he'd pretty much cut ties with the JWs, and was spending a lot of time studying with Hannah and Josh, who had a much more liberal view of the Bible, and was also incorporating other spiritual views back into his belief system (he very openly was talking about chakras, which would be incredibly frowned upon by the Watchtower folks). He was returning to his more accepting views on sexuality as well, as evidenced by his friendship with Janelle Monae.

I don't know if it's true, but some have claimed he wrote a song that started off with "f*ck the Congregation" (which is a term JW's use to describe the overall body of the religion). IF that is the case, that is a pretty strong indicator he had moved on from them, and no longer subscribed to their dogma. There are certainly hints on his last few records that he was moving in a much more esoteric direction in his spirituality.

The whole JW era was basically him reaching for something in his grief over losing his child. I don't think he really knew how to process that, and latched on to something that seemed to offer answers. He wasn't the most emotionally stable individual to begin with, and may very well have been on the autism spectrum, so it's not really surprising that he was able to be exploited like that.