I hope everyone's on the same page about the Tim Stoen - Jim Jones custody battle, which Stoen launched not for reasons of genuine emotion, but because it is the sort of thing operatives do when they want to turn the pages of reality. It looks to me like Jones is the biological father of the boy.
Jones wasn't going crazy, or letting his drug use get out of hand. He was being pushed into failure and manipulated into giving a semblance of a leader on the edge. Of course, as his charisma diminished, the real power became even more vested in that cabal of half-dozen witches, and like Susan Amos, it would be a coin toss to see if he were terminated as part of the experiment.
Then there's the old adage--be nice to everybody while you're on the way up, because you're probably going to see them again on the way down.