Question: The answer is not given in the film, but does it explain in the early scripts why Jack shot his parents but not Bruce? If not, what was Joe Chill's reason for shooting Thomas Wayne in Batman Begins?
Answer: It's unlikely there was anything specific in early script development addressing this. In the film, it was Jack Napier, not Joe Chill, who was the killer. He had plenty of time to shoot young Bruce, but hesitated, made a menacing remark, then was called away by his accomplice. In the Batman universe and the various interpretations, there's never been one definitive explanation. In the original lore, Bruce Wayne's parents were the victims of a random mugging by Joe Chill, who, for whatever reason, murdered the Waynes, probably spontaneously. Bruce was probably spared because many hesitate to kill a child. Chill may have considered Bruce too young to remember specific details. Something could have scared him off. However, this really has to be seen through the lens of a writer. The plot requires that Bruce survive the ordeal in order to grow up and become Batman. His parents' murders shaped and motivated everything in his life from that point on. Otherwise, there would be no story to tell.
Answer: With regards to Chill in Batman Begins, Thomas Wayne is shown reaching towards Chill when he grabs Martha to get her jewelry. Chill gets spooked and shoots Thomas. He then shoots Martha and runs off. Joe Chill is shown to be extremely nervous and on edge, and he doesn't appear to regard Bruce in any way at all; all he wants is the jewelry.
Answer: There's a fan theory that Bruce Wayne projects his parents' killer onto all his enemies, so whoever he's fighting at that particular moment killed his parents.
Question: How did the Joker's henchmen get to the top of the church? We don't see them enter the building. The only thing I can think of is they were dropped off by the helicopter, but then why wasn't the helicopter still there when the Joker, Batman, and Vicki Vale reached the top?
Answer: Actually, it is answered in the film. Jack did want to kill young Bruce because Jack had pointed his gun at him. When Jack's accomplice begged Jack to just leave the area, Jack walked away.