No, it could not have been saved, because the writers wrote themselves into a hole from which there was no escape, at least not within the confines of Trek.
I think you're spot on with your observation.
You can't do a movie about going to meet God and then not meet him, and in Trek you can't meet God. It's a good idea for a movie, but as a Star Trek movie it is doomed before pen is put to paper.
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. Regarding the ending, well... every
movie is predictable in that sense. Either the heroes will win, or they won't. But, they always do. Did anyone think that the Joker would win in Batman? Or that Titanic wouldn't sink? Yet they were both very good.