blowero, my major disappointment was that while both sides were gamely permitted to introduce arguments, Palmer Joss was given the last world. I’ll box it to be safe:
“Prove that you loved your daddy! Nyaahh!! Take that!” Any atheist as smart as Ellie is supposed to be should have been able to respond to that easily–except that you can’t actually make a movie that advocates atheism, no, so his flawed analogy leaves her flatfooted.
Also, as you suspect, the endings are quite different.
I’m always infuriated by the ending of the movie.
First off, because there is some proof supporting Ellie’s account. The 18 minutes of static on the tape demonstrates that in Ellie’s frame of reference, a significant amount of time passed.
Since they hid the evidence from her, though, Ellie had no proof and she has to have faith that her experience was genuine–although, really, if she has unshakeable faith in what occurred, then what’s happened is that a rational, scientific person has Gone Over to the Other Side. You can’t really tell whether this is the case from the film, IMHO. If she hasn’t lost it by the end of the film, she should feel distain for those those soppy people standing out on the stairs with their “We believe Ellie” signs. She admitted that she wouldn’t necessarily beleive her own story, if it hadn’t happened to her, so why should the blind, unreasoning faith of these people be a reassurance to her? Again, it’s not easy to tell what she really feels at this point in the film, though I have the sinking suspicion that the filmmakers meant it to be touching. I think that the mass audience is meant to come away with the notion that Ellie’s “arrogant” atheism has been conquered by her experience, and that annoys the hell out of me. Either Ann Druyan was asleep at the switch, or she made some big compromises, or she isn’t much of an atheist herself, but she failed to protect Sagan’s message, IMHO.
Anyway, in the book, the whole trip is quite different, and the book doesn’t end nearly so abruptly after Ellie’s journey. She does what a scientist should do–she continues to seek evidence. You’ll have to read the book to find out what she discovers, if anything. 
The book is overall more thoughtful and less sappy than the movie–it’s a thinking person’s novel, whereas . . . well, I’m not sure what the film is supposed to be. The book has no romatic relationship between Ellie and Joss, which was a relief, especially after the total lack of chemistry between Jodie Foster and Matthew McConaughey really sabotaged that part of the movie. And of course the astronomy/admnistration stuff about getting funding and instrument time, and the way that the telescopes were used, much of which was wrong in the movie, was done differently in the book. Sagan was, after all, a working astronomer. 
Whew–that was long. If anyone has a reply, maybe there should be a Contact thread?