Militarize them with what? All they had until they found the Pegasus was one ship destined to be mothballed using museum pieces for the fighter squadron. Why not have elections, you're attempting to save/ rebuild society, their society involved elections. If you want to be the good guys, be worthy of survival, you need to worry about the treatment of prisoners, and even in a full blown military dictatorship (which is what you're proposing) you don't execute prisoners until they've been tapped of data, there's more to be learned from Cylon prisoners than their biology. In a free society people can decide their directions, with only 50,000 people what is a low value unit?
How do you capture a Cylon raider? They got the one because of a lucky shot. You don't just capture enemy hardware (and enemy personel, remember Cylon raiders are both equipment and soldiers all in one) because you decide to, there's a lot of additional risk that goes into deliberately not using lethal force, risk you can't afford when then number of pilots you have can't even get your ready room to half full.
The Cylon interface thing was silly. Moore even said so. They do have a reliable test for them, but it's slow (11 hours per test).
I think the writers are doing fine. One or two serious flubs like the plug in thing but for the most part they are doing a good job of working within their defined universe. There were certain story concepts that were the goal of the series, like how does civilian government survive a massive disaster like this and rebuild a free society. One of the keys to the new BSG is in one conversation from mini-series when Rosaline explains to Adama that they already lost the war. Your complaints all come from Adama's position that as long as he had a gun the war wasn't over yet, but Adama was wrong the war was over the important thing now was survival.