There's definitely some play amongst both military and civilian as far as a representation of moral and ethical standards goes. I suppose the apt saying would be "the difference amongst the groups is larger than the difference between."
Continuing with the ideal, you have Scott as a paragon of the military. He's mostly level-headed, treats the civilians with respect (rather than a resource), has a sense of duty, and is generally well-liked. If Scott had been in charge, there probably wouldn't be a problem right now.
It's tempting to put Eli as a paragon of the civilians; I think that is a mistake (see below). I have to put forward Wray. She (seemingly) wants everyone to work together, generally non-combatant but still capable of holding her own, and generally reliable. Wray did what she had to in order to prevent a military dictatorship, using the resources she had, in a non-violent way. In essence, she's the representation of civilization on Earth, and wants to move it back that way. That the show is decidedly pro-military makes this more difficult to explain though.
On the extremist side, you have Young and Rush - each generally representing the worst of the military and civilians. Neither has respect for the other side, nor wants to work together. It's notable both are loners. You also have Greer and Chloe - the former the stereotypical military hot-head, and the latter the stereotypical civilian useless person. It's notable that they're both generally uncaring about the military/civilian divide despite taking sides. In the end, Greer is ultimately in the middle of Young and Scott, and Chloe is generally in between Rush and Wray.
Eli seems to be at the center of the conflict; in essence, he's a representation of Aristotle's phronimos (possibly spelled wrong), ie, the ideal middle ground. That he comes off as an idealist is not be coincidence - his position in the whole scheme of things is by definition ideal. Of course, making that work seems to be Eli's arc, of sorts. I would consider putting TJ in this category as well.
Anyway, about the episode, I found it generally likable. I found the use of the hole convenient, but a nice reference. It makes sense that Rush wouldn't know about the hole, and Wray might overlook it. I was expecting them to take a shuttle when they jumped out of FTL and go back around through the gate into the civilian side.
I was hoping Eli would be a little more against Young, given his comment in last week's episode to Young about getting rid of Rush. He showed another sign of it today, sticking up for Rush's shield plan.
TJ easily had the best line (paraphrased): "War is what we do." Completely bad-ass. Her nonchalant, almost tired, attitude about the whole thing was awesome as well. It's why I'm inclined to put her in Eli's group of idealists; she's tired of the whole military versus civilian thing.
It's about time they used the stones for something practical. That the connection was broken in the middle of the surgery was a little too convenient. I'm willing to give it a pass; Eli was guessing at the cause, it seems more likely the aliens blocked the stones from working.
My firm hope is that by the end of the season, both Rush and Young are confined, and the crew starts working together to survive. Survival isn't serviced by the conflict, nor by either side being in control. It's services by both sides working together.