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 think they had the right idea, to show a zealot so overshadowed by his own arrogance, that he led them right into a trap when he thought he was leading them to paradise.
I had origionally heard that they were trying to get Sean Connery to play Sybok, but he was contracted for Indiana Jones at the time, and had to turn down the part. I think it would have been fascinating to see how he could have brought life to the character.
When I look at this film, I just see the pieces of what could have been one of the best Trek films, but put together as one of the worst. I know the strike, really hurt the production of this film, and that's another factor that you have to consider. Alot of work done on this film was done by guys that had little or no experience, because they were filling in for the lockedout Union workers.