I've read this from Bennett numerous times, and it always sounded like a piss-poor excuse for how crap the film turned out, ie) not our fault.
Star Trek has dealt with the concept of God countless times, and has handled it well by and large.
There's a huge, huge difference between dealing with some "God" that is really just a powerful alien, and dealing with God without quotes, the God of Abraham, the God that some sizable portion of the audience believes in.
It is only the former "Gods" that Trek put on screen frequently. Other sci-fi/fantasy franchises have seriously handled the latter God, and sometimes handed it well, but not Trek.