Just watched this episode for the first time (all of them are to me since I've just started catching up). An interesting episode, but sort of silly, really. I enjoyed it the political debate between the "terrorist" and Apollo in the microcosm sense. Two guys talking about the notion of freedom (a term very close and dear to my heart) and government. Pretty interesting.
However, in the larger context, it is a stupid thing to be debating. Here you are, the last 47K humans in the universe (as far as you know), and 1500 convicted criminals are fussing about being treated like "free men". The terrorist demands that everyone be "free" in a place and time where "free" means absolutely nothing. Cylons are actively searching for you to complete the eradication of the human race, and this dude wants to talk about elections. Whilst I can definitely appreciate the notion of a free society, that society must be in a stable position to survive before it honestly be free.
The founding fathers had a similar issue when discussing slavery right after the Revolutionary War. The union was fragile and infantile...weak and uncertain. In-fighting between the states was likely to cause the whole thing to collapse. The northern states pushed to eradicate slavery and the southern states argued that it would basically destroy the economy and the southern way of life. The cooler heads in government at the time actually cause a resolution to be passed (Franklin proposed it, if I recall correctly) that forbade the discussion of the issue (slavery) until 1805. This was a tough choice made to allow the union to solidify and strengthen before tackling the issue. Historians surmise that the founders probably even realized that they were condemning the nation to what we call the Civil War, but it was the only way to keep the nation together. It had be strong enough to withstand the hurt without dying, to bend without breaking. Given the fact our society has existed all this time as a result, it's hard to argue with the logic.
I understand that the show is used often as a canvas on which to paint some basic ideas and view them...moving them around so we can all analyze them and talk about them. However, this wasn't, IMO, a good choice of time to showcase this particular issue.
Just my two cents.