An alternate ending idea
I think this movie would be better, and maybe even more poignant, if it took the extra leap and became an true apocalypse film (in Twilight Zone fashion).
They surface at the end and find that the U.S. has been absolutely devastated by a nuclear attack. So Hunter may have been morally correct, brave, and audacious to question the orders and to stand up to the captain and all that jazz...but his actions still cost millions of lives, maybe even lost the war. One of those ironic endings that flies in the face of the "always question the morality of your orders" mentality.
Somehow I think that ending may have stayed with us a bit more (like that kick in the guts ending to The Mist). Honestly, I found the existing ending, with a ho-hum lecture from Jason Robards about what a 'mess they made' and a casual stroll into retirement with a puppy dog a bit too wimpy for the dark and epic direction this movie could have taken.