I was concerned about this, but the flick does not seem to say much about God at all, so it’s really an agnostic materialism. There are philosophies better than this, but there are also philosophies much worse.
The portion of the novel given in the movie doesn't directly touch on it - you're absolutely right. But the entire thesis of Atlas Shrugged is an indirect attack on the message of the Cross.
The famous speech by John Galt near the end of the book - over 25,000 words and probably over three hours long if it were actually recited - is effectively an extended assault on the notion of the righteous sacrificing themselves for the good of sinners.
While the sequel will likely never be financed and while the producers would probably never inflict the full text of that wooden speech on an audience, they would not be true to the novel if they did not drive that point home - since that is the core thesis of the book and of Ayn Rand's whole notion of "the virtue of selfishness."
Frankly, I cannot think of a worse philosophy than one which excludes the Living God. I re-reading Atlas Shrugged. I first read it when it came out many years ago. I’m at the first chapter of Section II. But I doubt that Rand, an atheist, mentioned God in a positive way, if she mentioned Him at all.