The line about the God and patriotism was a bit heavy, but I took it as more trying to provoke a sense duty, almost to the point of indoctrinated propaganda, rather than signaling some shift towards a more religious administration.
I was sort of throw off a bit at the end by the talk about the importance of the island. The way the woman who's name I can't remember, was describing it, made me thing she was talking about the Island from Lost. I really hope they don't try and push in some sci-fi or fantasy elements. I would like the story to stay more of a military action/drama series.
I thought that overall, this last episode was better handled. The pacing felt more balanced and it seemed to handle all the story elements at least enough to give them all a few moments worth of coverage. I really like that they're actually going into the fallout and disruption of the crew who don't want to stay on the Sub. In many cases, it would be easy to simply focus on the struggle of the command crew and ignore the other officers and enlisted crew, for the sake of simply saying that everyone agrees that they're doing the right thing. That isn't the case here though and as Chaplin pointed out during the standoff, everyone has to decide for themselves where they stand. It may not be a big deal to some, but I give them a lot of credit for taking on that aspect of the story.
The petty thug guy is getting annoying though and not in the sense of him being a thorn in the side of the people we're supposed to be liking, but because he's such a non-interesting character. Nothing he does makes any sense which I guess is supposed to make him dangerous and unpredictable, but that's not compelling to me unless the character has the charm and style to pull it off, which this guy doesn't.
His control over the island doesn't appear to be in question, to the extent that Chaplin refuses to confront him, even though two Navy seals (only carrying pistols) had no trouble infiltrating his base and drawing down on him. They should have popped him and done everyone a favor.