I thought I would jump into the Wrath of Khan vs. Into Darkness discussion. I frankly do not like either film. Wrath of Khan was too morose for my taste because of the "brain bugs" (been long time since I've watched it, hence the lack of true name of the insect). Into the Darkness is equally disturbing in It's morbidity and focus on death. While Benedict Cumberbatch was a rather good villain, there are scenes like him crushing of a captain's skull that felt more than a little demonic. Granted such violence is warranted, it still felt like overkill.
I frankly was most offended by two scenes in Into Darkness. The first was the opening scene on the Class M planet with the white faced people and their worship of the Enterprise. This harkens to "Chariots of the gods" and has been the belief Hollywood has been using like propaganda in their films. The second offensive part was when Kirk pulls a Wrath of Khan Spock salvation of the Enterprise and the crewmembers (Chekov I believe says it) say "It's a miracle," and Spock responds "there are no such things." This was an obvious attack on a fundamental belief of the Christian faith. Christians believe in miracles in the time of Jesus and sects of Christianity believe (myself included) that they happen today.
Finally, I felt the philosophy of death in the film is completely anti-Judeo Christianity and any other monotheistic religion. The depiction is that you die and there is no afterlife, no heaven or hell. This is very Darwinist and Atheistic. It frankly ruined the film for me.
Well, SirG. I still have not seen this film, but allow me to make a few observations on the religious points you've mentioned:
First, Star Trek has always, ALWAYS, made a point of denouncing the validity of Christianity. This is evident when Dr. McCoy calls the events in Genesis a mythology in Star Trek II: The Wrath of Khan (this is during the discussion of the 'Genesis device'; McCoy says something to the effect of, "You don't believe the mythology that the world was created in 6 days, do you Mr. Spock?").
Second, Star Trek V: The Final Frontier is another excellent example of how the Trek writers regard Christianity.
Third, Kirk has always been more of an agnostic than anything. Does it matter if Kirk had no afterlife experience? I mean, good grief: I was just watching an episode of Voyager today, ("Emanations"), in which one of the Starfleet crewmembers denounced an afterlife. He basically stated that there is no real answer to the question, "is there an afterlife?". So that philosophy of no afterlife, whether it's heaven or hell, is something that has ALWAYS existed in the Trek universe. It just has. To become angry with ONE film over reiterating something that has been present since 1966 is kind of ridiculous (and it's ignoring a basic tenant of Trek philosophy).
No, I don't agree with a lot of the principles present in the Trek universe. Neither do I agree with most of what's present spiritually in the Star Wars universe. But it's there. At least Abrams got one thing apparently right: he has transferred [successfully] the spirituality created by Roddenberry into his own films.
Oh, and on the matter of the alien culture worshiping the Enterprise: this is also NOT new to the Trek universe. The only other example I can think of similar to this is the Voyager episode "In the Blink of an Eye", where Voyager is stuck in orbit above a planet, and they become the center of the culture's religious views. This is just the one off the top of my head; I'm sure there are others scattered throughout the franchise.