Many, many years of watching military science fiction has taught us that captains and commanders and people in uniforms always know best. SG-1 invariably portrayed civilian oversight as being thoroughly corrupt and incompetent. We cheered on Jack O'Neal and his noble team of unbeatable soldiers, even as they casually went around suppressing free speech with gag orders whenever a civilian learned anything about the Stargate.This "evil" thing is utterly unfathomable to me. How is it that the military guys are "good"? If I was a civilian on the ship -- and especially if I knew about Rush being left on that planet -- the only evil I'd see is the military, who have proven they'll sacrifice you for being inconvenient.
In SGU, we're shown that we should look favorably upon handsome, daring young soldier Scott, father-figure Young, and caregiver T.J. Greer is a thug and bully, but note that he's never really taken to task for it, either by Young or by TV-show karma, which lends his bad-boy attitude validity.
Rush and Camile Wray are the foremost represenatives of the civilian segment, and they are predominantly self-serving in their every action, even when they try to obfuscate their motives by claiming they're looking out for the whole. Perhaps even more damning is that in spite of their pragmatic intelligence, they lose every confrontation. Karma delivers them come-uppance, so this teaches viewers they are in the wrong. Then there are all of the other civilians, who are a bunch of selfish, petulant whiners.
So, maybe it isn't so hard to see why supporting the civilian takeover is viewed as "evil".