Sounds like you've got a smart kid. I would just warn you again not to underestimate the power of social pressure over an extended period of time. It's probably better for him to know your father is full of BS before getting pseudo-logical answers from him. Though in this day and age information is much more readily available to disprove things than it was when I was in his position.
In the end, I suspect you'll be fine either way, even if he does end up slightly indoctrinated for a time. When he hits his teens he won't want anything to do with the cult, and if you support that there's almost no way he'll get sucked in. At that point the most important thing is to ensure he has healthy coping mechanisms for difficulty so that he won't turn to the cult for answers.
Sounds like you're doing something right, though, so just keep it up!